Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr3
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: 42799318
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 891409 characters in sequence are not A, C, G, or T
File 17 of 141
Found at i:5125562 original size:85 final size:84
Alignment explanation
Indices: 5125418--5125626 Score: 296
Period size: 85 Copynumber: 2.5 Consensus size: 84
5125408 CTTGTGATGA
* *** *
5125418 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTATTTAAGTGTCGCTAAAGAACATGATC
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTTTAAGCACCACTAAAGAACATGATC
5125483 TTTAGCGGCGTTTTTT-TCT
66 TTTAGCGGCGTTTTTTAT-T
*
5125502 AAGCGCCGCTAAAGAACATGATCTTTAGCTGCGTCTTTTTTTTAAGCACCACTAAAGAACATGAT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGT-TTTTTTTTAAGCACCACTAAAGAACATGAT
*
5125567 CTTTAGTGGCGTTTTTTATT
65 CTTTAGCGGCGTTTTTTATT
* *
5125587 AAACGCCGCTAAAGAGCATGA-CTTTTAGCGGCGTTTTTTT
1 AAGCGCCGCTAAAGAACATGATC-TTTAGCGGCGTTTTTTT
5125627 GTAAACGCTG
Statistics
Matches: 112, Mismatches: 10, Indels: 6
0.88 0.08 0.05
Matches are distributed among these distances:
84 40 0.36
85 71 0.63
86 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.35
Consensus pattern (84 bp):
AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTTTAAGCACCACTAAAGAACATGATC
TTTAGCGGCGTTTTTTATT
Found at i:5125634 original size:42 final size:41
Alignment explanation
Indices: 5125418--5125626 Score: 285
Period size: 42 Copynumber: 5.0 Consensus size: 41
5125408 CTTGTGATGA
5125418 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTATTT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTT-TTT
* *
5125460 AAGTGTCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTT-T
*
5125502 AAGCGCCGCTAAAGAACATGATCTTTAGCTGCGTCTTTTTTTT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCG--TTTTTTTT
* * *
5125545 AAGCACCACTAAAGAACATGATCTTTAGTGGCGTTTTTTATT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTT-TT
* *
5125587 AAACGCCGCTAAAGAGCATGA-CTTTTAGCGGCGTTTTTTT
1 AAGCGCCGCTAAAGAACATGATC-TTTAGCGGCGTTTTTTT
5125627 GTAAACGCTG
Statistics
Matches: 148, Mismatches: 14, Indels: 11
0.86 0.08 0.06
Matches are distributed among these distances:
41 10 0.07
42 101 0.68
43 30 0.20
44 7 0.05
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.35
Consensus pattern (41 bp):
AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTT
Found at i:5130707 original size:14 final size:14
Alignment explanation
Indices: 5130690--5130719 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5130680 ATTCATAAAT
5130690 AATATTATATCAAA
1 AATATTATATCAAA
*
5130704 AATATTATTTCAAA
1 AATATTATATCAAA
5130718 AA
1 AA
5130720 GATAGGTAAT
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:0.57, C:0.07, G:0.00, T:0.37
Consensus pattern (14 bp):
AATATTATATCAAA
Found at i:5133116 original size:3 final size:3
Alignment explanation
Indices: 5133104--5133153 Score: 59
Period size: 3 Copynumber: 17.3 Consensus size: 3
5133094 GTTTTTTTCA
** *
5133104 ATT ATT -TT ATT ATT ATT ATT ATT ATT ATT A-T ACC ATT ATT AGT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
5133150 ATT A
1 ATT A
5133154 CATTACTTAC
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
2 4 0.10
3 36 0.90
ACGTcount: A:0.34, C:0.04, G:0.02, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:5133403 original size:13 final size:12
Alignment explanation
Indices: 5133385--5133414 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
5133375 CTCCATAGTT
5133385 TATTTATATATTA
1 TATTTATATA-TA
5133398 TATTTATATATA
1 TATTTATATATA
5133410 TATTT
1 TATTT
5133415 TTTGTTCTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.41
13 10 0.59
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (12 bp):
TATTTATATATA
Found at i:5135031 original size:17 final size:17
Alignment explanation
Indices: 5135005--5135040 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
5134995 GTGTGTTTTG
*
5135005 TTTTGGCTGCATGACAT
1 TTTTGACTGCATGACAT
5135022 TTTTGACTGCATGACAT
1 TTTTGACTGCATGACAT
5135039 TT
1 TT
5135041 CATCATAGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.19, C:0.17, G:0.19, T:0.44
Consensus pattern (17 bp):
TTTTGACTGCATGACAT
Found at i:5135719 original size:41 final size:41
Alignment explanation
Indices: 5135657--5135739 Score: 139
Period size: 41 Copynumber: 2.0 Consensus size: 41
5135647 AACAGTATCA
*
5135657 GAAGGAGATGCAAGACCGACTTCAGCTACAGGTGCAAGAGC
1 GAAGGAGATGCAAGACCGACTTCAGCTACAAGTGCAAGAGC
* *
5135698 GAAGGAGATGCAAGACTGACTTCAGCTACAAGTGCAGGAGC
1 GAAGGAGATGCAAGACCGACTTCAGCTACAAGTGCAAGAGC
5135739 G
1 G
5135740 GTTAGACAAG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.34, C:0.20, G:0.33, T:0.13
Consensus pattern (41 bp):
GAAGGAGATGCAAGACCGACTTCAGCTACAAGTGCAAGAGC
Found at i:5137475 original size:21 final size:21
Alignment explanation
Indices: 5137450--5137492 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
5137440 AATGTTCTTT
5137450 CATTCTTTAT-GACTTTTTTTC
1 CATTCTTT-TGGACTTTTTTTC
*
5137471 CATTCTTTTGGATTTTTTTTC
1 CATTCTTTTGGACTTTTTTTC
5137492 C
1 C
5137493 TGCCAGACCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 1 0.05
21 19 0.95
ACGTcount: A:0.12, C:0.19, G:0.07, T:0.63
Consensus pattern (21 bp):
CATTCTTTTGGACTTTTTTTC
Found at i:5138457 original size:7 final size:7
Alignment explanation
Indices: 5138432--5138464 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
5138422 AGTGATGTGA
5138432 AAAAATG
1 AAAAATG
5138439 AAAAGATG
1 AAAA-ATG
5138447 -AAAATG
1 AAAAATG
5138453 AAAAATG
1 AAAAATG
5138460 AAAAA
1 AAAAA
5138465 GTAAAAATAG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
6 3 0.12
7 18 0.75
8 3 0.12
ACGTcount: A:0.73, C:0.00, G:0.15, T:0.12
Consensus pattern (7 bp):
AAAAATG
Found at i:5138471 original size:21 final size:21
Alignment explanation
Indices: 5138432--5138472 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
5138422 AGTGATGTGA
*
5138432 AAAAATGAAAAGATGAAAATG
1 AAAAATGAAAAGATAAAAATG
5138453 AAAAATGAAAA-AGTAAAAAT
1 AAAAATGAAAAGA-TAAAAAT
5138473 AGAGAGGCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.71, C:0.00, G:0.15, T:0.15
Consensus pattern (21 bp):
AAAAATGAAAAGATAAAAATG
Found at i:5139868 original size:89 final size:89
Alignment explanation
Indices: 5139718--5140442 Score: 812
Period size: 89 Copynumber: 8.1 Consensus size: 89
5139708 GAGTAGCAGT
* **
5139718 AGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAA-AAATTAGATCTTGTCTTCATGTAC
1 AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATC-AAAGAAAACAGATCTTGTCTTCATGTAC
* *
5139782 TGGCGTGAAGTAGATCAAAGATAAT
65 TGGCGTGAAGTAGATCAAAGAAAAC
* * * *
5139807 AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCATATCCTGTCTTCATGTACT
1 AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCAAAGAAAACAGATCTTGTCTTCATGTACT
* *
5139872 GGCGTGAAGTAGATCAAAGATAGC
66 GGCGTGAAGTAGATCAAAGAAAAC
* * ** *
5139896 AGATCTTGTCTTCCCATACTGGTGGCGAAATAGATCGAAGAAAGTAGATCTTGTCTTCATGTATT
1 AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCAAAGAAAACAGATCTTGTCTTCATGTACT
*
5139961 GGCGTGAAGTAGATCGAAGAAAAC
66 GGCGTGAAGTAGATCAAAGAAAAC
*** * * ***
5139985 AGATCTTGTCTTCATGTACTGG-CGTGAAGTAGATCAAAGAAAACAGATCTTGTCTTCCCATACT
1 AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCAAAGAAAACAGATCTTGTCTTCATGTACT
* * ** *
5140049 GGTGGCGAAGTAGATTGAAGAAAAT
66 GG-CGTGAAGTAGATCAAAGAAAAC
*** * * ***
5140074 AGATCTTGTCTTCATGTACTGGT-GTGAAGTAGATCAAAGAAAATAGATCTTGTCTTCCCATACT
1 AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCAAAGAAAACAGATCTTGTCTTCATGTACT
* * *
5140138 GGTGGCGAAGTAGATCGAAGAAAAC
66 GG-CGTGAAGTAGATCAAAGAAAAC
*** * * * *
5140163 AGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTACT
1 AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCAAAGAAAACAGATCTTGTCTTCATGTACT
5140227 GGCGTGAAGTAGATCAAAGAAAAC
66 GGCGTGAAGTAGATCAAAGAAAAC
* *
5140251 AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCAAAGAAAACAAATCTTGTCCTCATGTACT
1 AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCAAAGAAAACAGATCTTGTCTTCATGTACT
*
5140316 GGTGTGAAGTAGATCAAAGAAAAC
66 GGCGTGAAGTAGATCAAAGAAAAC
* * * * ***
5140340 AAATCTTGTCTTCCCATACTGGTGACGAAGTAGATCAAAGATAACAGATCTTGCCTTCCCATACT
1 AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCAAAGAAAACAGATCTTGTCTTCATGTACT
* * *
5140405 GGTG-GCAAAGCAGATCGAAGAAAAC
66 GGCGTG--AAGTAGATCAAAGAAAAC
*
5140430 AGATCTTATCTTC
1 AGATCTTGTCTTC
5140443 ATGTATTGGC
Statistics
Matches: 561, Mismatches: 68, Indels: 13
0.87 0.11 0.02
Matches are distributed among these distances:
88 74 0.13
89 460 0.82
90 27 0.05
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.28
Consensus pattern (89 bp):
AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCAAAGAAAACAGATCTTGTCTTCATGTACT
GGCGTGAAGTAGATCAAAGAAAAC
Found at i:5139970 original size:133 final size:134
Alignment explanation
Indices: 5139718--5140442 Score: 751
Period size: 133 Copynumber: 5.4 Consensus size: 134
5139708 GAGTAGCAGT
* * * ** ***
5139718 AGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAA-AAATTAGATCTTGTCTTCATGTAC
1 AGATCTTGTCTTCACATACTGGTCGCGAAGTAGATC-AAAGAAAACAGATCTTGTCTTCCCATAC
* * * * *** * * *
5139782 TGG-CGTGAAGTAGATCAAAGATAATAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAA
65 TGGTGGCGAAGTAGATCGAAGAAAATAGATCTTGTCTTCATGTACTGG-CGTGAAGTAGATCAAA
*
5139846 GAAAGC
129 GAAAAC
* * ** * * *
5139852 ATATCCTGTCTTCATGTACTGG-CGTGAAGTAGATCAAAGATAGCAGATCTTGTCTTCCCATACT
1 AGATCTTGTCTTCACATACTGGTCGCGAAGTAGATCAAAGAAAACAGATCTTGTCTTCCCATACT
* * * *
5139916 GGTGGCGAAATAGATCGAAGAAAGTAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGA
66 GGTGGCGAAGTAGATCGAAGAAAATAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGA
5139981 AAAC
131 AAAC
** *
5139985 AGATCTTGTCTTCATGTACTGG-CGTGAAGTAGATCAAAGAAAACAGATCTTGTCTTCCCATACT
1 AGATCTTGTCTTCACATACTGGTCGCGAAGTAGATCAAAGAAAACAGATCTTGTCTTCCCATACT
* *
5140049 GGTGGCGAAGTAGATTGAAGAAAATAGATCTTGTCTTCATGTACTGGTGTGAAGTAGATCAAAGA
66 GGTGGCGAAGTAGATCGAAGAAAATAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGA
*
5140114 AAAT
131 AAAC
* * * *** *
5140118 AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTATT
1 AGATCTTGTCTTCACATACTGGTCGCGAAGTAGATCAAAGAAAACAGATCTTGTCTTCCCATACT
* * *
5140183 GG-CGTGAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGA
66 GGTGGCGAAGTAGATCGAAGAAAATAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGA
5140247 AAAC
131 AAAC
* * * * ***
5140251 AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCAAAGAAAACAAATCTTGTCCTCATGTACT
1 AGATCTTGTCTTCACATACTGGTCGCGAAGTAGATCAAAGAAAACAGATCTTGTCTTCCCATACT
* * * * *** * *
5140316 GGT-GTGAAGTAGATCAAAGAAAACAAATCTTGTCTTCCCATACTGGTGACGAAGTAGATCAAAG
66 GGTGGCGAAGTAGATCGAAGAAAATAGATCTTGTCTTCATGTACTGGCG-TGAAGTAGATCAAAG
*
5140380 ATAAC
130 AAAAC
* * * * * * *
5140385 AGATCTTGCCTTCCCATACTGGTGGCAAAGCAGATCGAAGAAAACAGATCTTATCTTC
1 AGATCTTGTCTTCACATACTGGTCGCGAAGTAGATCAAAGAAAACAGATCTTGTCTTC
5140443 ATGTATTGGC
Statistics
Matches: 515, Mismatches: 71, Indels: 10
0.86 0.12 0.02
Matches are distributed among these distances:
132 3 0.01
133 355 0.69
134 157 0.30
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.28
Consensus pattern (134 bp):
AGATCTTGTCTTCACATACTGGTCGCGAAGTAGATCAAAGAAAACAGATCTTGTCTTCCCATACT
GGTGGCGAAGTAGATCGAAGAAAATAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGA
AAAC
Found at i:5140128 original size:222 final size:222
Alignment explanation
Indices: 5139718--5140463 Score: 1111
Period size: 222 Copynumber: 3.4 Consensus size: 222
5139708 GAGTAGCAGT
* * *
5139718 AGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAA-AAAATTAGATCTTGTCTTCATGTAC
1 AGATCTTGTCTTCACATACTGG-CGTGAAGTAGATCGAAGAAAA-CAGATCTTGTCTTCATGTAC
* *
5139782 TGGCGTGAAGTAGATCAAAGATAATAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAG
64 TGGCGTGAAGTAGATCAAAGAAAACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAG
* * * * * *
5139847 AAAGCATATCCTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAGCAGATCTTGTCTTCCCA
129 AAAACAAATCTTGTCTTCATGTACTGGTGTGAAGTAGATCAAAGAAAACAGATCTTGTCTTCCCA
* *
5139912 TACTGGTGGCGAAATAGATCGAAGAAAGT
194 TACTGGTGGCGAAGTAGATCGAAGAAAGC
** *
5139941 AGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTACTG
1 AGATCTTGTCTTCACATACTGGCGTGAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTACTG
*
5140006 GCGTGAAGTAGATCAAAGAAAACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATTGAAGAA
66 GCGTGAAGTAGATCAAAGAAAACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAA
* * *
5140071 AATAGATCTTGTCTTCATGTACTGGTGTGAAGTAGATCAAAGAAAATAGATCTTGTCTTCCCATA
131 AACAAATCTTGTCTTCATGTACTGGTGTGAAGTAGATCAAAGAAAACAGATCTTGTCTTCCCATA
*
5140136 CTGGTGGCGAAGTAGATCGAAGAAAAC
196 CTGGTGGCGAAGTAGATCGAAGAAAGC
** *
5140163 AGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTACTG
1 AGATCTTGTCTTCACATACTGGCGTGAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTACTG
*
5140228 GCGTGAAGTAGATCAAAGAAAACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCAAAGAA
66 GCGTGAAGTAGATCAAAGAAAACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAA
* *
5140293 AACAAATCTTGTCCTCATGTACTGGTGTGAAGTAGATCAAAGAAAACAAATCTTGTCTTCCCATA
131 AACAAATCTTGTCTTCATGTACTGGTGTGAAGTAGATCAAAGAAAACAGATCTTGTCTTCCCATA
* *
5140358 CTGGTGACGAAGTAGATCAAAGATAA-C
196 CTGGTGGCGAAGTAGATCGAAGA-AAGC
* * * * * *
5140385 AGATCTTGCCTTCCCATACTGGTG-GCAAAGCAGATCGAAGAAAACAGATCTTATCTTCATGTAT
1 AGATCTTGTCTTCACATACTGGCGTG--AAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTAC
5140449 TGGCGTGAAGTAGAT
64 TGGCGTGAAGTAGAT
5140464 TGAAGATTAC
Statistics
Matches: 481, Mismatches: 38, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
221 1 0.00
222 407 0.85
223 73 0.15
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.28
Consensus pattern (222 bp):
AGATCTTGTCTTCACATACTGGCGTGAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTACTG
GCGTGAAGTAGATCAAAGAAAACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAA
AACAAATCTTGTCTTCATGTACTGGTGTGAAGTAGATCAAAGAAAACAGATCTTGTCTTCCCATA
CTGGTGGCGAAGTAGATCGAAGAAAGC
Found at i:5140673 original size:132 final size:132
Alignment explanation
Indices: 5140459--5140696 Score: 449
Period size: 132 Copynumber: 1.8 Consensus size: 132
5140449 TGGCGTGAAG
*
5140459 TAGATTGAAGATTACAGATCTTTTCTCCCTAAGCAATAGTGGAGCAGATCAAAGATGGTGGATTT
1 TAGATTGAAGATTACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCAAAGATGGTGGATTT
5140524 TACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAACAGTGG
66 TACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAACAGTGG
5140589 AA
131 AA
* *
5140591 TAGATTGAAGATTACAGATCTTATCTCCCTATGCAGTAGTGGAGCAGATCAAAGATGGTGGATTT
1 TAGATTGAAGATTACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCAAAGATGGTGGATTT
5140656 TACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAA
66 TACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAA
5140697 CGTAACACCC
Statistics
Matches: 103, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
132 103 1.00
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.28
Consensus pattern (132 bp):
TAGATTGAAGATTACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCAAAGATGGTGGATTT
TACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAACAGTGG
AA
Found at i:5142107 original size:40 final size:40
Alignment explanation
Indices: 5142077--5142262 Score: 259
Period size: 40 Copynumber: 4.7 Consensus size: 40
5142067 GCTACTCGTT
* *
5142077 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
5142117 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
5142157 CAAATCCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * * * *
5142197 CAAATGCCTTCGGGAGTTAACCCGAATTTGGTCACTTAGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAAC-TCGCA
*
5142238 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
5142263 CATCATTCAA
Statistics
Matches: 132, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
40 122 0.92
41 10 0.08
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:5145770 original size:13 final size:12
Alignment explanation
Indices: 5145752--5145781 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
5145742 CTCCATAGTT
5145752 TATTTATATATTA
1 TATTTATATA-TA
5145765 TATTTATATATA
1 TATTTATATATA
5145777 TATTT
1 TATTT
5145782 TTTGTTCTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.41
13 10 0.59
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (12 bp):
TATTTATATATA
Found at i:5147238 original size:16 final size:16
Alignment explanation
Indices: 5147201--5147245 Score: 60
Period size: 16 Copynumber: 3.0 Consensus size: 16
5147191 GTGTAAAAGG
5147201 ATAAAG-AAATAAT-A
1 ATAAAGTAAATAATAA
*
5147215 A-CAAGTAAATAATAA
1 ATAAAGTAAATAATAA
5147230 ATAAAGTAAATAATAA
1 ATAAAGTAAATAATAA
5147246 TAATAATAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
13 3 0.12
14 8 0.31
15 2 0.08
16 13 0.50
ACGTcount: A:0.69, C:0.02, G:0.07, T:0.22
Consensus pattern (16 bp):
ATAAAGTAAATAATAA
Found at i:5150073 original size:18 final size:18
Alignment explanation
Indices: 5150022--5150064 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
5150012 GAAACTCTAT
5150022 ATCCTTCTGGGATTTTAA
1 ATCCTTCTGGGATTTTAA
5150040 ATCCTTCTGGGATTTTAA
1 ATCCTTCTGGGATTTTAA
5150058 ATCCTTC
1 ATCCTTC
5150065 AGGAATTTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.21, C:0.21, G:0.14, T:0.44
Consensus pattern (18 bp):
ATCCTTCTGGGATTTTAA
Found at i:5155029 original size:23 final size:23
Alignment explanation
Indices: 5155003--5155055 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
5154993 ATAAGTGACA
5155003 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
5155026 CACTGAAATGTAGCCTAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
5155049 CACTGAT
1 CACTGAT
5155056 CAATAACACT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.23
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:5156444 original size:17 final size:17
Alignment explanation
Indices: 5156399--5156446 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 17
5156389 TATTTTTTCA
*
5156399 TAATTTTTATAATTTTG
1 TAATTTTTAAAATTTTG
5156416 TAATAATTTTAAAGATTTT-
1 TAAT--TTTTAAA-ATTTTG
5156435 TAATTTTTAAAA
1 TAATTTTTAAAA
5156447 ATAGTTTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
16 1 0.04
17 11 0.41
19 10 0.37
20 5 0.19
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (17 bp):
TAATTTTTAAAATTTTG
Found at i:5156473 original size:8 final size:9
Alignment explanation
Indices: 5156400--5156486 Score: 65
Period size: 9 Copynumber: 9.2 Consensus size: 9
5156390 ATTTTTTCAT
*
5156400 AATTTTTAT
1 AATTTTTAA
5156409 AATTTTGTAA
1 AATTTT-TAA
5156419 TAA-TTTTAA
1 -AATTTTTAA
5156428 AGATTTTT--
1 A-ATTTTTAA
5156436 AATTTTTAAAA
1 AATTTTT--AA
5156447 ATAGTTTTTATA
1 A-A-TTTTTA-A
5156459 AATTTTTAA
1 AATTTTTAA
5156468 AATTTTTAA
1 AATTTTTAA
5156477 AA-TTTTAA
1 AATTTTTAA
5156485 AA
1 AA
5156487 AATTAATTAA
Statistics
Matches: 66, Mismatches: 1, Indels: 23
0.73 0.01 0.26
Matches are distributed among these distances:
7 6 0.09
8 10 0.15
9 22 0.33
10 15 0.23
11 5 0.08
12 3 0.05
13 5 0.08
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (9 bp):
AATTTTTAA
Found at i:5157504 original size:10 final size:10
Alignment explanation
Indices: 5157489--5157526 Score: 58
Period size: 10 Copynumber: 3.8 Consensus size: 10
5157479 ATATTTTATT
5157489 ATAATTTTTA
1 ATAATTTTTA
*
5157499 ATAATTTATA
1 ATAATTTTTA
*
5157509 TTAATTTTTA
1 ATAATTTTTA
5157519 ATAATTTT
1 ATAATTTT
5157527 CAAATGATTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (10 bp):
ATAATTTTTA
Found at i:5165762 original size:30 final size:30
Alignment explanation
Indices: 5165721--5165810 Score: 153
Period size: 30 Copynumber: 3.0 Consensus size: 30
5165711 TCAGTTAATT
5165721 AATAAAGTATGGGTCAAATATGTCTAGATA
1 AATAAAGTATGGGTCAAATATGTCTAGATA
* *
5165751 AATAAAATATGGATCAAATATGTCTAGATA
1 AATAAAGTATGGGTCAAATATGTCTAGATA
*
5165781 AATAAAGTATTGGTCAAATATGTCTAGATA
1 AATAAAGTATGGGTCAAATATGTCTAGATA
5165811 CTCTCATAAT
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 55 1.00
ACGTcount: A:0.46, C:0.07, G:0.17, T:0.31
Consensus pattern (30 bp):
AATAAAGTATGGGTCAAATATGTCTAGATA
Found at i:5168937 original size:16 final size:16
Alignment explanation
Indices: 5168916--5168974 Score: 55
Period size: 16 Copynumber: 3.6 Consensus size: 16
5168906 ATACAATTTT
5168916 TTTATTTTATATATAA
1 TTTATTTTATATATAA
* *
5168932 TTTATTCTATATGTAA
1 TTTATTTTATATATAA
* * *
5168948 TTTTTTTTGTACATACAA
1 -TTTATTT-TATATATAA
5168966 TTTATTTTA
1 TTTATTTTA
5168975 AAGATTTGTA
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
16 16 0.48
17 11 0.33
18 6 0.18
ACGTcount: A:0.31, C:0.05, G:0.03, T:0.61
Consensus pattern (16 bp):
TTTATTTTATATATAA
Found at i:5170307 original size:26 final size:27
Alignment explanation
Indices: 5170285--5170336 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
5170275 ACCAAAAATT
*
5170285 TATTTTAAAA-ATAAAAAATAAAAAAG
1 TATTTTAAAATAAAAAAAATAAAAAAG
5170311 TATTTTAAAATAAAAAAAATAAAAAA
1 TATTTTAAAATAAAAAAAATAAAAAA
5170337 TATATATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 10 0.42
27 14 0.58
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (27 bp):
TATTTTAAAATAAAAAAAATAAAAAAG
Found at i:5171454 original size:13 final size:13
Alignment explanation
Indices: 5171436--5171460 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5171426 AAAAACAACT
5171436 TTTTCAAAAAATA
1 TTTTCAAAAAATA
5171449 TTTTCAAAAAAT
1 TTTTCAAAAAAT
5171461 CTGCCAAGCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (13 bp):
TTTTCAAAAAATA
Found at i:5171566 original size:34 final size:35
Alignment explanation
Indices: 5171508--5171574 Score: 118
Period size: 34 Copynumber: 1.9 Consensus size: 35
5171498 CAAACACCAG
5171508 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
*
5171543 AAAATATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAATATTTTCCAGTAAATCATTTTACAGAAAA
5171575 TATTTTACTG
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 17 0.55
35 14 0.45
ACGTcount: A:0.46, C:0.12, G:0.09, T:0.33
Consensus pattern (35 bp):
AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:5172772 original size:14 final size:14
Alignment explanation
Indices: 5172755--5172795 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
5172745 ATAAATTTGT
5172755 AAAAATAAAAAT-A
1 AAAAATAAAAATAA
5172768 AAAAATAAAAAATAA
1 AAAAAT-AAAAATAA
*
5172783 AAAAATATAAATA
1 AAAAATAAAAATA
5172796 TAGATCACAC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
13 6 0.24
14 12 0.48
15 7 0.28
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (14 bp):
AAAAATAAAAATAA
Found at i:5172789 original size:8 final size:7
Alignment explanation
Indices: 5172755--5172786 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
5172745 ATAAATTTGT
5172755 AAAAAT-
1 AAAAATA
5172761 AAAAATA
1 AAAAATA
5172768 AAAAATA
1 AAAAATA
5172775 AAAAATA
1 AAAAATA
5172782 AAAAA
1 AAAAA
5172787 ATATAAATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.24
7 19 0.76
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAATA
Found at i:5172862 original size:14 final size:14
Alignment explanation
Indices: 5172845--5172885 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
5172835 ATAAATTTGT
5172845 AAAAATAAAAAT-A
1 AAAAATAAAAATAA
5172858 AAAAATAAAAAATAA
1 AAAAAT-AAAAATAA
*
5172873 AAAAATATAAATA
1 AAAAATAAAAATA
5172886 TAGATATATG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
13 6 0.24
14 12 0.48
15 7 0.28
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (14 bp):
AAAAATAAAAATAA
Found at i:5172879 original size:8 final size:7
Alignment explanation
Indices: 5172845--5172876 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
5172835 ATAAATTTGT
5172845 AAAAAT-
1 AAAAATA
5172851 AAAAATA
1 AAAAATA
5172858 AAAAATA
1 AAAAATA
5172865 AAAAATA
1 AAAAATA
5172872 AAAAA
1 AAAAA
5172877 ATATAAATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.24
7 19 0.76
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAATA
Found at i:5172940 original size:18 final size:18
Alignment explanation
Indices: 5172919--5172955 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
5172909 AAGTTATAAA
5172919 ATGTAAATATATATAAGT
1 ATGTAAATATATATAAGT
*
5172937 ATGTATATATATATAAGT
1 ATGTAAATATATATAAGT
5172955 A
1 A
5172956 AATTATGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.11, T:0.41
Consensus pattern (18 bp):
ATGTAAATATATATAAGT
Found at i:5180461 original size:30 final size:30
Alignment explanation
Indices: 5180427--5180489 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
5180417 TCTTAACAAG
5180427 CAAATGCCTCTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
* *
5180457 CAAATGCCTTTAAAATAATAACAAGATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
5180487 CAA
1 CAA
5180490 TAAAATAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.56, C:0.16, G:0.05, T:0.24
Consensus pattern (30 bp):
CAAATGCCTCTAAAATAATAACAAAATTAA
Found at i:5189788 original size:61 final size:59
Alignment explanation
Indices: 5189723--5189835 Score: 165
Period size: 61 Copynumber: 1.9 Consensus size: 59
5189713 AGTGATTATT
* * *
5189723 TTAATATTAAATTTAATTTAATGTTTATAT-TATAGATAAATATTCTATTAATTTCATCAGA
1 TTAATATTAAATTTAATCTAATATTT-TATCT-T-GATAAATATTATATTAATTTCATCAGA
5189784 TTAATATTAAATTTAATCTAATATTTTATCTTGATAAATATTATATTAATTT
1 TTAATATTAAATTTAATCTAATATTTTATCTTGATAAATATTATATTAATTT
5189836 AATATTAAAG
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
59 19 0.40
60 4 0.08
61 25 0.52
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.51
Consensus pattern (59 bp):
TTAATATTAAATTTAATCTAATATTTTATCTTGATAAATATTATATTAATTTCATCAGA
Found at i:5192108 original size:38 final size:38
Alignment explanation
Indices: 5192058--5192131 Score: 148
Period size: 38 Copynumber: 1.9 Consensus size: 38
5192048 GAGATGAGAC
5192058 TTTTTGTAGGAATCACTCTTTGAAGTTGATTTTAACAT
1 TTTTTGTAGGAATCACTCTTTGAAGTTGATTTTAACAT
5192096 TTTTTGTAGGAATCACTCTTTGAAGTTGATTTTAAC
1 TTTTTGTAGGAATCACTCTTTGAAGTTGATTTTAAC
5192132 TCCCATCTTC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.26, C:0.11, G:0.16, T:0.47
Consensus pattern (38 bp):
TTTTTGTAGGAATCACTCTTTGAAGTTGATTTTAACAT
Found at i:5194258 original size:17 final size:17
Alignment explanation
Indices: 5194236--5194292 Score: 55
Period size: 16 Copynumber: 3.5 Consensus size: 17
5194226 ATATACAAAA
5194236 GAAAAATAATATTATAT
1 GAAAAATAATATTATAT
* * *
5194253 GAAAAATATTATCAT-G
1 GAAAAATAATATTATAT
*
5194269 GAAATATAATA-TATAT
1 GAAAAATAATATTATAT
*
5194285 AAAAAATA
1 GAAAAATA
5194293 TACAAAGGAT
Statistics
Matches: 30, Mismatches: 9, Indels: 3
0.71 0.21 0.07
Matches are distributed among these distances:
15 2 0.07
16 15 0.50
17 13 0.43
ACGTcount: A:0.60, C:0.02, G:0.07, T:0.32
Consensus pattern (17 bp):
GAAAAATAATATTATAT
Found at i:5194583 original size:11 final size:11
Alignment explanation
Indices: 5194567--5194612 Score: 51
Period size: 11 Copynumber: 4.4 Consensus size: 11
5194557 AGAGCTTAGC
*
5194567 TAAAATTGAAA
1 TAAAATTAAAA
5194578 TAAAATTAAAA
1 TAAAATTAAAA
* *
5194589 GAAAAATAAAA
1 TAAAATTAAAA
5194600 T-AAA-TAAAA
1 TAAAATTAAAA
5194609 TAAA
1 TAAA
5194613 TAATCGAACG
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
9 6 0.20
10 5 0.17
11 19 0.63
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.22
Consensus pattern (11 bp):
TAAAATTAAAA
Found at i:5194606 original size:9 final size:9
Alignment explanation
Indices: 5194575--5194615 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
5194565 GCTAAAATTG
5194575 AAATAAAATT
1 AAATAAAA-T
*
5194585 AAA-AGAA-
1 AAATAAAAT
5194592 AAATAAAAT
1 AAATAAAAT
5194601 AAATAAAAT
1 AAATAAAAT
5194610 AAATAA
1 AAATAA
5194616 TCGAACGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
7 3 0.11
8 3 0.11
9 18 0.67
10 3 0.11
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (9 bp):
AAATAAAAT
Found at i:5195447 original size:10 final size:10
Alignment explanation
Indices: 5195402--5195458 Score: 66
Period size: 11 Copynumber: 5.7 Consensus size: 10
5195392 CGAATGTGCA
5195402 AAAAATCAAAT
1 AAAAAT-AAAT
5195413 AAAAATCAAAT
1 AAAAAT-AAAT
5195424 AAAAATAAAT
1 AAAAATAAAT
5195434 --AAATAAAT
1 AAAAATAAAT
5195442 AAAAAT-AAT
1 AAAAATAAAT
5195451 AGAAAATA
1 A-AAAATA
5195459 TCTCTTTGTC
Statistics
Matches: 42, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
8 8 0.19
9 4 0.10
10 13 0.31
11 17 0.40
ACGTcount: A:0.75, C:0.04, G:0.02, T:0.19
Consensus pattern (10 bp):
AAAAATAAAT
Found at i:5196310 original size:44 final size:43
Alignment explanation
Indices: 5196149--5196533 Score: 158
Period size: 45 Copynumber: 8.8 Consensus size: 43
5196139 AGATTTATGA
* * * *
5196149 TTTTAATCCGCTCCACTGCAACTTTAGGGAGATAGGAT-TGATT
1 TTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTG-TG
** * *
5196192 TCTTTTGTATGCTCCACTGCAACTTCAGGGAGATAAGA-CT-AG
1 T-TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTG
* *** * ** *
5196234 ATGCGATCTGCTCTACTGCAACTTCAAAGAGATAATATCTGTGG
1 TTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGT-G
*
5196278 TTTTAATCTGCTCCACTGCAACTTCAGGGAGATAGGAT-TCGT-
1 TTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATCT-GTG
** * *
5196320 TTCTTCTGTCTGCTCCACTGCAACTTCAGGCAGATAAGA-CT-AG
1 TT-TT-AATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTG
* *** * * *
5196363 ATGCGATCTGCTCTACTGTAACTTCAGAGAGATAAGA-CT-TG
1 TTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTG
* * * * * *
5196404 CTATCGTCAATCCGCTCCACTGTAACTTCAGGGAGATAGGATTTGCTA
1 -T-T--TTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTG-TG
* * ** * * * *
5196452 TCTTCAGTCTGCTCTGCTGCAACTTCAGGAAGATAGGATTTGCTA
1 T-TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTG-TG
* * ** *
5196497 TCTTCAGTCTGCTCTGCTGTAACTTCAGGGAGATAAG
1 T-TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAG
5196534 GTTCGCCATC
Statistics
Matches: 263, Mismatches: 62, Indels: 32
0.74 0.17 0.09
Matches are distributed among these distances:
41 57 0.22
42 4 0.02
43 6 0.02
44 93 0.35
45 99 0.38
46 1 0.00
47 2 0.01
48 1 0.00
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.31
Consensus pattern (43 bp):
TTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTG
Found at i:5196362 original size:129 final size:128
Alignment explanation
Indices: 5196105--5196486 Score: 473
Period size: 129 Copynumber: 3.0 Consensus size: 128
5196095 ACTGAGGTTT
* * * * *
5196105 GATGCGATCTGCTATACGGCAA-TTCATAGAGATGAGATTTATGATTTTAATCCGCTCCACTGCA
1 GATGCGATCTGCTCTACTGCAACTTCAAAGAGATAAGATCT-TGATTTTAATCCGCTCCACTGCA
* * * *
5196169 ACTTTAGGGAGATAGGATTGATTTCTTTTGTATGCTCCACTGCAACTTCAGGGAGATAAGACTA
65 ACTTCAGGGAGATAGGATTGATTTCTTCTGTCTGCTCCACTGCAACTTCAGGAAGATAAGACTA
* * *
5196233 GATGCGATCTGCTCTACTGCAACTTCAAAGAGATAATATCTGTGGTTTTAATCTGCTCCACTGCA
1 GATGCGATCTGCTCTACTGCAACTTCAAAGAGATAAGATCT-TGATTTTAATCCGCTCCACTGCA
*
5196298 ACTTCAGGGAGATAGGATTCG-TTTCTTCTGTCTGCTCCACTGCAACTTCAGGCAGATAAGACTA
65 ACTTCAGGGAGATAGGATT-GATTTCTTCTGTCTGCTCCACTGCAACTTCAGGAAGATAAGACTA
* * * *
5196362 GATGCGATCTGCTCTACTGTAACTTCAGAGAGATAAGA-CTTGCTATCGTCAATCCGCTCCACTG
1 GATGCGATCTGCTCTACTGCAACTTCAAAGAGATAAGATCTTG--AT-TTTAATCCGCTCCACTG
* * * * **
5196426 TAACTTCAGGGAGATAGGATTTGCTATCTTCAGTCTGCTCTGCTGCAACTTCAGGAAGATA
63 CAACTTCAGGGAGATAGGA-TTGATTTCTTCTGTCTGCTCCACTGCAACTTCAGGAAGATA
5196487 GGATTTGCTA
Statistics
Matches: 221, Mismatches: 26, Indels: 11
0.86 0.10 0.04
Matches are distributed among these distances:
127 2 0.01
128 22 0.10
129 129 0.58
130 34 0.15
131 34 0.15
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.31
Consensus pattern (128 bp):
GATGCGATCTGCTCTACTGCAACTTCAAAGAGATAAGATCTTGATTTTAATCCGCTCCACTGCAA
CTTCAGGGAGATAGGATTGATTTCTTCTGTCTGCTCCACTGCAACTTCAGGAAGATAAGACTA
Found at i:5196431 original size:45 final size:44
Alignment explanation
Indices: 5196282--5196591 Score: 233
Period size: 45 Copynumber: 7.1 Consensus size: 44
5196272 CTGTGGTTTT
* * *
5196282 AATCTGCTCCACTGCAACTTCAGGGAGATAGGA-TT-CGTTTCTTC
1 AATCTGCTCCACTGTAACTTCA-GGAGATAAGACTTGC-TATCTTC
** * * *
5196326 TGTCTGCTCCACTGCAACTTCAGGCAGATAAGACTAG--A--TGC
1 AATCTGCTCCACTGTAACTTCAGG-AGATAAGACTTGCTATCTTC
* * *
5196367 GATCTGCTCTACTGTAACTTCAGAGAGATAAGACTTGCTATCGTC
1 AATCTGCTCCACTGTAACTTCAG-GAGATAAGACTTGCTATCTTC
* * *
5196412 AATCCGCTCCACTGTAACTTCAGGGAGATAGGATTTGCTATCTTC
1 AATCTGCTCCACTGTAACTTCA-GGAGATAAGACTTGCTATCTTC
* ** * * *
5196457 AGTCTGCTCTGCTGCAACTTCAGGAAGATAGGATTTGCTATCTTC
1 AATCTGCTCCACTGTAACTTCAGG-AGATAAGACTTGCTATCTTC
* ** * * *
5196502 AGTCTGCTCTGCTGTAACTTCAGGGAGATAAG-GTTCGCCATCTTT
1 AATCTGCTCCACTGTAACTTCA-GGAGATAAGACTT-GCTATCTTC
* *
5196547 AGTCTGC-CCACTGTAACTTCAGG-GATAAGACTTGCTTTCTTC
1 AATCTGCTCCACTGTAACTTCAGGAGATAAGACTTGCTATCTTC
5196589 AAT
1 AAT
5196592 TTTAACGCTA
Statistics
Matches: 217, Mismatches: 36, Indels: 28
0.77 0.13 0.10
Matches are distributed among these distances:
41 32 0.15
42 15 0.07
43 7 0.03
44 43 0.20
45 117 0.54
46 3 0.01
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.31
Consensus pattern (44 bp):
AATCTGCTCCACTGTAACTTCAGGAGATAAGACTTGCTATCTTC
Found at i:5197143 original size:259 final size:259
Alignment explanation
Indices: 5196593--5197876 Score: 1677
Period size: 259 Copynumber: 4.9 Consensus size: 259
5196583 TTCTTCAATT
* * * * *** *
5196593 TTAACG-CTAGGGAGATAAGATTCGCTGCCTTAAGCTTTAATCTGCTCTGCTACAGTGCTAGGGA
1 TTAACGAC-AGGGAGATAAGATTCGCTGCCCTCAGCTTTAATCTGCTCCGCTGCAACACCAGGGA
* * * * *
5196657 AACCAGATTCGCTATCTTTAGCCTTAATCCGTTCCACTATAATGCCAAAGAGATTGGATTCGCTG
65 AACCAGATTCGCTACCTTTAGCTTTAATCTGTTCCACTGTAATGCCAAAGAGATAGGATTCGCTG
* * * * *
5196722 CCCT-TAGCTTTAATCCACTCCACTTCAACTATTCCATTCCACTGCAA-GTCAGGGAAACAAGAT
130 -CCTACAGCTTTAATCCGCTCCACTTCAGCTATTTCATTCCACTGCAACGCCAGGGAAACAAGAT
* * *
5196785 TTGCTACCTTTAGCTTTAATCTGTTCCACTGCAACACCAGGGAAGTAAGACTGGTTACTTTCAGT
194 TCGCTACCTTTAGCTTTAATCTGTTCCACTGCAACGCCAGGGAAGTAAGACTGGTTACTCTCAGT
5196850 C
259 C
* * * *
5196851 TTAACGACAGGGAGGTAAGATTCGCTACCCTCAGCTTTAATTTGCTCCGTTGCAACACCAGGGAA
1 TTAACGACAGGGAGATAAGATTCGCTGCCCTCAGCTTTAATCTGCTCCGCTGCAACACCAGGGAA
* * * *
5196916 ACCAGATTCGCTACCTTTAGCTTTAATCTGTTCTACTGAAATACCAAAGAGATAGGATTTGCTGC
66 ACCAGATTCGCTACCTTTAGCTTTAATCTGTTCCACTGTAATGCCAAAGAGATAGGATTCGCTGC
* * * *
5196981 CTACAGCTGTAATCCACTCCACTTCAGCTATTTCATTCCACTACAACGCCCGGGAAACAAGATTC
131 CTACAGCTTTAATCCGCTCCACTTCAGCTATTTCATTCCACTGCAACGCCAGGGAAACAAGATTC
* * * *
5197046 GATACCTTTAGCTTTAATCTGTTCC-CTTGCAACGTCAGAGAAGTAAGACTGGTTACTCTCAATC
196 GCTACCTTTAGCTTTAATCTGTTCCAC-TGCAACGCCAGGGAAGTAAGACTGGTTACTCTCAGTC
* *
5197110 TTAA-AACCAGGGAGATAAGATTCGTTGCCCTCAGCTTTAATCTGCTCCGCTGCAACACCAGGGA
1 TTAACGA-CAGGGAGATAAGATTCGCTGCCCTCAGCTTTAATCTGCTCCGCTGCAACACCAGGGA
* * * *
5197174 AATCAAATTCGCTACCTTTAGGTTTAATCTATTCCACTGTAATGCCAAAGAGATAGGATTCGCTG
65 AACCAGATTCGCTACCTTTAGCTTTAATCTGTTCCACTGTAATGCCAAAGAGATAGGATTCGCTG
* * * *
5197239 CCCACAGCTTTAATCCGCTCCACTTCAGCT-TTAATCTATTCCACTGCAGCGCCAAGGAAATAAG
130 CCTACAGCTTTAATCCGCTCCACTTCAGCTATT--TC-ATTCCACTGCAACGCCAGGGAAACAAG
* * *
5197303 ATTCGCTACCTTTAGCTTTAATCTGTTCCACTACAACACCAGGGAAGTAAGACTGGTTACTTTCA
192 ATTCGCTACCTTTAGCTTTAATCTGTTCCACTGCAACGCCAGGGAAGTAAGACTGGTTACTCTCA
5197368 GTC
257 GTC
* * * * * *
5197371 TTAACGACAGGGAGGTATGATTCACTGCCCTCAGCTTTAATTTGTTTCGCTGCAACACCAGGGAA
1 TTAACGACAGGGAGATAAGATTCGCTGCCCTCAGCTTTAATCTGCTCCGCTGCAACACCAGGGAA
* *
5197436 ACCAGGTTCGCTACCTTTAGCTTTAATCTGTTCTACTGTAATGCCAAAGAGATAGGATTCGCTGC
66 ACCAGATTCGCTACCTTTAGCTTTAATCTGTTCCACTGTAATGCCAAAGAGATAGGATTCGCTGC
* *
5197501 CTACAGCTGTAATCCGCTCCACTTCAGCTATTTCATTCCACTACAACGTCC-GGGAAACAAGATT
131 CTACAGCTTTAATCCGCTCCACTTCAGCTATTTCATTCCACTGCAACG-CCAGGGAAACAAGATT
* * * * * *
5197565 CGCTACCTTTAGCTTTAATCTGTTCCCCTGCGACGTCAGAGAAATAAGACTGATTACTCTCAGTC
195 CGCTACCTTTAGCTTTAATCTGTTCCACTGCAACGCCAGGGAAGTAAGACTGGTTACTCTCAGTC
** ** * * *
5197630 TTAAC-ACCAATGAGATAAGATTCGCTATCCTCAACTTTAATCTGCTTCGCTGCAAGACCAGGGA
1 TTAACGA-CAGGGAGATAAGATTCGCTGCCCTCAGCTTTAATCTGCTCCGCTGCAACACCAGGGA
** *
5197694 AATTAGATTCGCTACCTTTAGCTTTAATCTATTCCACTGTAATGCCAAAGAGATAGGATTCGCTG
65 AACCAGATTCGCTACCTTTAGCTTTAATCTGTTCCACTGTAATGCCAAAGAGATAGGATTCGCTG
* *
5197759 CCCACAGCTTTAATCCGCTCCACTTCAGCT-TTAATCTATTCCACTGCAACGCTAGGGAAACAAG
130 CCTACAGCTTTAATCCGCTCCACTTCAGCTATT--TC-ATTCCACTGCAACGCCAGGGAAACAAG
* *
5197823 ATTCGCTACCTTTAACTTTAATCTGTTCCACTACAACGCCAGGGAAGTAAGACT
192 ATTCGCTACCTTTAGCTTTAATCTGTTCCACTGCAACGCCAGGGAAGTAAGACT
5197877 AGTGTCTTCA
Statistics
Matches: 889, Mismatches: 120, Indels: 31
0.85 0.12 0.03
Matches are distributed among these distances:
257 3 0.00
258 151 0.17
259 430 0.48
260 9 0.01
261 292 0.33
262 4 0.00
ACGTcount: A:0.28, C:0.26, G:0.17, T:0.29
Consensus pattern (259 bp):
TTAACGACAGGGAGATAAGATTCGCTGCCCTCAGCTTTAATCTGCTCCGCTGCAACACCAGGGAA
ACCAGATTCGCTACCTTTAGCTTTAATCTGTTCCACTGTAATGCCAAAGAGATAGGATTCGCTGC
CTACAGCTTTAATCCGCTCCACTTCAGCTATTTCATTCCACTGCAACGCCAGGGAAACAAGATTC
GCTACCTTTAGCTTTAATCTGTTCCACTGCAACGCCAGGGAAGTAAGACTGGTTACTCTCAGTC
Found at i:5197281 original size:21 final size:21
Alignment explanation
Indices: 5197243--5197288 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
5197233 TCGCTGCCCA
* *
5197243 CAGCTTTAATCCGCTCCACTT
1 CAGCTTTAATCCACTCCACTG
* *
5197264 CAGCTTTAATCTATTCCACTG
1 CAGCTTTAATCCACTCCACTG
5197285 CAGC
1 CAGC
5197289 GCCAAGGAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.22, C:0.35, G:0.11, T:0.33
Consensus pattern (21 bp):
CAGCTTTAATCCACTCCACTG
Found at i:5197556 original size:520 final size:519
Alignment explanation
Indices: 5196601--5197876 Score: 1980
Period size: 520 Copynumber: 2.5 Consensus size: 519
5196591 TTTTAACGCT
* * * * *** * *
5196601 AGGGAGATAAGATTCGCTGCCTTAAGCTTTAATCTGCTCTGCTACAGTGCTAGGGAAACCAGATT
1 AGGGAGATAAGATTCGCTGCCCTCAGCTTTAATCTGCTCCGCTGCAACACCAGGGAAATCAGATT
* * ** * * **
5196666 CGCTATCTTTAGCCTTAATCCGTTCCACTATAATGCCAAAGAGATTGGATTCGCTGCCCTTAGCT
66 CGCTACCTTTAGCTTTAATCTATTCCACTGTAATGCCAAAGAGATAGGATTCGCTGCCCACAGCT
* * * * * * *
5196731 TTAATCCACTCCACTTCAAC--TATTCCATTCCACTGCAAGTCAGGGAAACAAGATTTGCTACCT
131 TTAATCCGCTCCACTTCAGCTTTAATCTATTCCACTGCACGCCAGGGAAACAAGATTCGCTACCT
*
5196794 TTAGCTTTAATCTGTTCCACTGCAACACCAGGGAAGTAAGACTGGTTACTTTCAGTCTTAACGAC
196 TTAGCTTTAATCTGTTCCACTACAACACCAGGGAAGTAAGACTGGTTACTTTCAGTCTTAACGAC
* *
5196859 AGGGAGGTAAGATTCGCTACCCTCAGCTTTAATTTGCTCCGTTGCAACACCAGGGAAACCAGATT
261 AGGGAGGTAAGATTCACTACCCTCAGCTTTAATTTGCTCCGCTGCAACACCAGGGAAACCAGATT
*
5196924 CGCTACCTTTAGCTTTAATCTGTTCTACTGAAATACCAAAGAGATAGGATTTGCTGCCTACAGCT
326 CGCTACCTTTAGCTTTAATCTGTTCTACTGAAATACCAAAGAGATAGGATTCGCTGCCTACAGCT
5196989 GTAATCCACTCCACTTCAGCTATTTCATTCCACTACAACGCCCGGGAAACAAGATTCGATACCTT
391 GTAATCCACTCCACTTCAGCTATTTCATTCCACTACAACGCCCGGGAAACAAGATTCGATACCTT
* * *
5197054 TAGCTTTAATCTGTTCCCTTGCAACGTCAGAGAAGTAAGACTGGTTACTCTCAATCTTAAAACC
456 TAGCTTTAATCTGTTCCCCTGCAACGTCAGAGAAATAAGACTGATTACTCTCAATCTTAAAACC
* *
5197118 AGGGAGATAAGATTCGTTGCCCTCAGCTTTAATCTGCTCCGCTGCAACACCAGGGAAATCAAATT
1 AGGGAGATAAGATTCGCTGCCCTCAGCTTTAATCTGCTCCGCTGCAACACCAGGGAAATCAGATT
*
5197183 CGCTACCTTTAGGTTTAATCTATTCCACTGTAATGCCAAAGAGATAGGATTCGCTGCCCACAGCT
66 CGCTACCTTTAGCTTTAATCTATTCCACTGTAATGCCAAAGAGATAGGATTCGCTGCCCACAGCT
* *
5197248 TTAATCCGCTCCACTTCAGCTTTAATCTATTCCACTGCAGCGCCAAGGAAATAAGATTCGCTACC
131 TTAATCCGCTCCACTTCAGCTTTAATCTATTCCACTGCA-CGCCAGGGAAACAAGATTCGCTACC
5197313 TTTAGCTTTAATCTGTTCCACTACAACACCAGGGAAGTAAGACTGGTTACTTTCAGTCTTAACGA
195 TTTAGCTTTAATCTGTTCCACTACAACACCAGGGAAGTAAGACTGGTTACTTTCAGTCTTAACGA
* * * * *
5197378 CAGGGAGGTATGATTCACTGCCCTCAGCTTTAATTTGTTTCGCTGCAACACCAGGGAAACCAGGT
260 CAGGGAGGTAAGATTCACTACCCTCAGCTTTAATTTGCTCCGCTGCAACACCAGGGAAACCAGAT
* *
5197443 TCGCTACCTTTAGCTTTAATCTGTTCTACTGTAATGCCAAAGAGATAGGATTCGCTGCCTACAGC
325 TCGCTACCTTTAGCTTTAATCTGTTCTACTGAAATACCAAAGAGATAGGATTCGCTGCCTACAGC
* * *
5197508 TGTAATCCGCTCCACTTCAGCTATTTCATTCCACTACAACGTCCGGGAAACAAGATTCGCTACCT
390 TGTAATCCACTCCACTTCAGCTATTTCATTCCACTACAACGCCCGGGAAACAAGATTCGATACCT
* * *
5197573 TTAGCTTTAATCTGTTCCCCTGCGACGTCAGAGAAATAAGACTGATTACTCTCAGTCTTAACACC
455 TTAGCTTTAATCTGTTCCCCTGCAACGTCAGAGAAATAAGACTGATTACTCTCAATCTTAAAACC
** ** * * * *
5197638 AATGAGATAAGATTCGCTATCCTCAACTTTAATCTGCTTCGCTGCAAGACCAGGGAAATTAGATT
1 AGGGAGATAAGATTCGCTGCCCTCAGCTTTAATCTGCTCCGCTGCAACACCAGGGAAATCAGATT
5197703 CGCTACCTTTAGCTTTAATCTATTCCACTGTAATGCCAAAGAGATAGGATTCGCTGCCCACAGCT
66 CGCTACCTTTAGCTTTAATCTATTCCACTGTAATGCCAAAGAGATAGGATTCGCTGCCCACAGCT
*
5197768 TTAATCCGCTCCACTTCAGCTTTAATCTATTCCACTGCAACGCTAGGGAAACAAGATTCGCTACC
131 TTAATCCGCTCCACTTCAGCTTTAATCTATTCCACTGC-ACGCCAGGGAAACAAGATTCGCTACC
* *
5197833 TTTAACTTTAATCTGTTCCACTACAACGCCAGGGAAGTAAGACT
195 TTTAGCTTTAATCTGTTCCACTACAACACCAGGGAAGTAAGACT
5197877 AGTGTCTTCA
Statistics
Matches: 690, Mismatches: 65, Indels: 5
0.91 0.09 0.01
Matches are distributed among these distances:
517 128 0.19
519 15 0.02
520 546 0.79
521 1 0.00
ACGTcount: A:0.28, C:0.26, G:0.17, T:0.29
Consensus pattern (519 bp):
AGGGAGATAAGATTCGCTGCCCTCAGCTTTAATCTGCTCCGCTGCAACACCAGGGAAATCAGATT
CGCTACCTTTAGCTTTAATCTATTCCACTGTAATGCCAAAGAGATAGGATTCGCTGCCCACAGCT
TTAATCCGCTCCACTTCAGCTTTAATCTATTCCACTGCACGCCAGGGAAACAAGATTCGCTACCT
TTAGCTTTAATCTGTTCCACTACAACACCAGGGAAGTAAGACTGGTTACTTTCAGTCTTAACGAC
AGGGAGGTAAGATTCACTACCCTCAGCTTTAATTTGCTCCGCTGCAACACCAGGGAAACCAGATT
CGCTACCTTTAGCTTTAATCTGTTCTACTGAAATACCAAAGAGATAGGATTCGCTGCCTACAGCT
GTAATCCACTCCACTTCAGCTATTTCATTCCACTACAACGCCCGGGAAACAAGATTCGATACCTT
TAGCTTTAATCTGTTCCCCTGCAACGTCAGAGAAATAAGACTGATTACTCTCAATCTTAAAACC
Found at i:5197801 original size:21 final size:21
Alignment explanation
Indices: 5197763--5197803 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
5197753 TCGCTGCCCA
*
5197763 CAGCTTTAATCCGCTCCACTT
1 CAGCTTTAATCCACTCCACTT
* *
5197784 CAGCTTTAATCTATTCCACT
1 CAGCTTTAATCCACTCCACT
5197804 GCAACGCTAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.22, C:0.34, G:0.07, T:0.37
Consensus pattern (21 bp):
CAGCTTTAATCCACTCCACTT
Found at i:5207751 original size:14 final size:15
Alignment explanation
Indices: 5207727--5207757 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
5207717 CATCAAATAA
5207727 AAATAAAATAAAAAT
1 AAATAAAATAAAAAT
5207742 AAAT-AAATAAAAAT
1 AAATAAAATAAAAAT
5207756 AA
1 AA
5207758 TAGAAAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (15 bp):
AAATAAAATAAAAAT
Found at i:5211046 original size:30 final size:31
Alignment explanation
Indices: 5211012--5211079 Score: 84
Period size: 30 Copynumber: 2.2 Consensus size: 31
5211002 TTGTCCAAGA
** * **
5211012 GTAAATACTCAAAATTTGAGGGATTAA-AGT
1 GTAAATACAAAAAATTTGAAGGACCAATAGT
5211042 GTAAATACAAAAAATTTGAAGGACCAATAGT
1 GTAAATACAAAAAATTTGAAGGACCAATAGT
5211073 GTAAATA
1 GTAAATA
5211080 TTTTACGGGT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 22 0.69
31 10 0.31
ACGTcount: A:0.49, C:0.07, G:0.18, T:0.26
Consensus pattern (31 bp):
GTAAATACAAAAAATTTGAAGGACCAATAGT
Found at i:5220092 original size:21 final size:21
Alignment explanation
Indices: 5220049--5220095 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
5220039 ACTCCCAGTT
*
5220049 AAAAAACTAAATATGCAATAA
1 AAAAAACTAAATATGCAAGAA
*
5220070 AAAAATACTAAAT-TGCTAGAA
1 AAAAA-ACTAAATATGCAAGAA
5220091 AAAAA
1 AAAAA
5220096 GCTCTTTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 16 0.70
22 7 0.30
ACGTcount: A:0.66, C:0.09, G:0.06, T:0.19
Consensus pattern (21 bp):
AAAAAACTAAATATGCAAGAA
Found at i:5227626 original size:43 final size:43
Alignment explanation
Indices: 5227579--5227722 Score: 130
Period size: 43 Copynumber: 3.3 Consensus size: 43
5227569 ACCGCTAAGG
*
5227579 GTCATGTTGTTTAGCAGCGCTTT-TATAGCAAACG-TCACTAAAA
1 GTCATGTTCTTTAGCAGCG-TTTCTATAGCAAACGCT-ACTAAAA
* * *
5227622 GTCATGTTCTTTAGCGGCGTTTCTATAGCAAACGCTGCTAAAG
1 GTCATGTTCTTTAGCAGCGTTTCTATAGCAAACGCTACTAAAA
* ** ** * ** *
5227665 GTCATGTTCATTAGTGGCACTTCTATAGCAAACCCCGCTAAAG
1 GTCATGTTCTTTAGCAGCGTTTCTATAGCAAACGCTACTAAAA
*
5227708 GTCATGTTCATTAGC
1 GTCATGTTCTTTAGC
5227723 GACTCTTTTT
Statistics
Matches: 88, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
42 3 0.03
43 84 0.95
44 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.32
Consensus pattern (43 bp):
GTCATGTTCTTTAGCAGCGTTTCTATAGCAAACGCTACTAAAA
Found at i:5228094 original size:21 final size:21
Alignment explanation
Indices: 5228067--5228137 Score: 88
Period size: 21 Copynumber: 3.4 Consensus size: 21
5228057 GTGCTTTCTG
*
5228067 CTCTGCTTCCCTCGCTGCTGC
1 CTCTGCTTCCCTCGCTACTGC
* * *
5228088 CTTTGCTTCTCTCGCTATTGC
1 CTCTGCTTCCCTCGCTACTGC
*
5228109 CTCTACTTCCCTCGCTACTGC
1 CTCTGCTTCCCTCGCTACTGC
*
5228130 ATCTGCTT
1 CTCTGCTT
5228138 TAAGTTGTAG
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.06, C:0.41, G:0.14, T:0.39
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTACTGC
Found at i:5230421 original size:9 final size:9
Alignment explanation
Indices: 5230407--5230596 Score: 66
Period size: 9 Copynumber: 20.2 Consensus size: 9
5230397 TAAGTATAAT
5230407 TAAGTTATG
1 TAAGTTATG
5230416 TAAGTTATG
1 TAAGTTATG
5230425 TAAGTTATG
1 TAAGTTATG
* * *
5230434 TGACTTACG
1 TAAGTTATG
5230443 TAAGTTATG
1 TAAGTTATG
* *
5230452 ATATGATATATA
1 -TAAG-T-TATG
* *
5230464 TAAGTAATT
1 TAAGTTATG
*
5230473 TAAGATT-TT
1 TAAG-TTATG
5230482 TAAGTATGTATG
1 TAAG--T-TATG
*
5230494 TGAGTTATG
1 TAAGTTATG
5230503 TAAGTTATG
1 TAAGTTATG
* * *
5230512 ATATGATATA
1 -TAAGTTATG
*
5230522 T-ATTTATG
1 TAAGTTATG
5230530 T-A-TTATG
1 TAAGTTATG
*
5230537 TAAGCTATG
1 TAAGTTATG
* *
5230546 TATTTGTTTTG
1 TA--AGTTATG
5230557 TAAGTTATGG
1 TAAGTTAT-G
* *
5230567 TATGATATATA
1 TAAG-T-TATG
5230578 TAAGTTAT-
1 TAAGTTATG
5230586 TAAGTTATG
1 TAAGTTATG
5230595 TA
1 TA
5230597 TGTGAGTTAT
Statistics
Matches: 134, Mismatches: 31, Indels: 32
0.68 0.16 0.16
Matches are distributed among these distances:
7 6 0.04
8 14 0.10
9 70 0.52
10 19 0.14
11 15 0.11
12 10 0.07
ACGTcount: A:0.34, C:0.02, G:0.18, T:0.46
Consensus pattern (9 bp):
TAAGTTATG
Found at i:5230922 original size:73 final size:77
Alignment explanation
Indices: 5230774--5230936 Score: 228
Period size: 73 Copynumber: 2.2 Consensus size: 77
5230764 AAATTGAAAT
* *
5230774 ATAATTAATTTGTCTATATTTATCAAAATAAGTAAAATATATATATAAAAAAAAAGACTTTGAGT
1 ATAAATAATTTGTCTATATTTATCAAAATAAGTAAAATATATATATAAAAAAAAAGACTTGGAGT
*
5230839 TAGCATTACAAG
66 TAGCATTACAAA
*
5230851 ATACAATAATTTGTCTATATTTATCAAAATAAGT-TAA-AT-TA-A-AAAAAAAAAGACTTGGAG
1 ATA-AATAATTTGTCTATATTTATCAAAATAAGTAAAATATATATATAAAAAAAAAGACTTGGAG
*
5230911 TTGGCATTACAAA
65 TTAGCATTACAAA
5230924 ATAAATATATTTG
1 ATAAATA-ATTTG
5230937 GCAAAATAAT
Statistics
Matches: 79, Mismatches: 5, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
72 4 0.05
73 36 0.46
74 1 0.01
75 2 0.03
76 2 0.03
77 5 0.06
78 29 0.37
ACGTcount: A:0.49, C:0.07, G:0.10, T:0.34
Consensus pattern (77 bp):
ATAAATAATTTGTCTATATTTATCAAAATAAGTAAAATATATATATAAAAAAAAAGACTTGGAGT
TAGCATTACAAA
Found at i:5231128 original size:66 final size:66
Alignment explanation
Indices: 5231054--5231192 Score: 163
Period size: 66 Copynumber: 2.1 Consensus size: 66
5231044 TATAAAATCG
* * * * *
5231054 ATAATTTATT-AAATTACATAAAAAATTGATCATTTCTTGACATAAAATCAAATAAACTAATCAA
1 ATAATTTATTCAAATTA-ATAAAAAATCGATAATTTATTCACATAAAACCAAATAAACTAATCAA
5231118 AC
65 AC
* ** * * *
5231120 ATAATTTATTCAATTTAATCGAAAATCGATAATTTATTCACATTAAACCGAATAAAGTAATCAAA
1 ATAATTTATTCAAATTAATAAAAAATCGATAATTTATTCACATAAAACCAAATAAACTAATCAAA
5231185 C
66 C
5231186 ATAATTT
1 ATAATTT
5231193 TTTTTCAATT
Statistics
Matches: 61, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
66 56 0.92
67 5 0.08
ACGTcount: A:0.49, C:0.12, G:0.04, T:0.35
Consensus pattern (66 bp):
ATAATTTATTCAAATTAATAAAAAATCGATAATTTATTCACATAAAACCAAATAAACTAATCAAA
C
Found at i:5231436 original size:14 final size:13
Alignment explanation
Indices: 5231407--5231449 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
5231397 AACTCCCTTT
5231407 TAAAACTCAAAA-A
1 TAAAACT-AAAATA
5231420 TAATAACTAAAATA
1 TAA-AACTAAAATA
*
5231434 TAAAGCTAAAATA
1 TAAAACTAAAATA
5231447 TAA
1 TAA
5231450 CCATACAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
13 19 0.70
14 8 0.30
ACGTcount: A:0.65, C:0.09, G:0.02, T:0.23
Consensus pattern (13 bp):
TAAAACTAAAATA
Found at i:5234110 original size:7 final size:7
Alignment explanation
Indices: 5234098--5234331 Score: 123
Period size: 7 Copynumber: 32.9 Consensus size: 7
5234088 ACTAATTAAT
5234098 CTAAACC
1 CTAAACC
5234105 CTAAACCC
1 CTAAA-CC
* *
5234113 CTAATTCT
1 CTAA-ACC
5234121 CTAAACC
1 CTAAACC
5234128 CTAAACTC
1 CTAAAC-C
5234136 CT-AACC
1 CTAAACC
*
5234142 CTTAACCC
1 C-TAAACC
5234150 CTAAACC
1 CTAAACC
*
5234157 TTAAACC
1 CTAAACC
*
5234164 C-CAACAC
1 CTAAAC-C
5234171 CTAAACC
1 CTAAACC
*
5234178 TTAAACC
1 CTAAACC
5234185 CTAAACC
1 CTAAACC
*
5234192 GTAAACC
1 CTAAACC
** *
5234199 AGAATCC
1 CTAAACC
5234206 CTAAACC
1 CTAAACC
*
5234213 CATAATCC
1 C-TAAACC
*
5234221 ATAAACC
1 CTAAACC
* **
5234228 TTAAATA
1 CTAAACC
*
5234235 GT-AACTC
1 CTAAAC-C
*
5234242 ATAAACC
1 CTAAACC
*
5234249 TTAAACC
1 CTAAACC
*
5234256 ATAAACC
1 CTAAACC
*
5234263 ATAAACC
1 CTAAACC
* *
5234270 ATAATCC
1 CTAAACC
5234277 CTAAACC
1 CTAAACC
*
5234284 CTAAATC
1 CTAAACC
* *
5234291 TTAAAAC
1 CTAAACC
*
5234298 ATAAACC
1 CTAAACC
* *
5234305 ATATACC
1 CTAAACC
5234312 CTAAACC
1 CTAAACC
*
5234319 ATAAACC
1 CTAAACC
5234326 CTAAAC
1 CTAAAC
5234332 TATAATGATA
Statistics
Matches: 173, Mismatches: 44, Indels: 20
0.73 0.19 0.08
Matches are distributed among these distances:
6 7 0.04
7 137 0.79
8 29 0.17
ACGTcount: A:0.44, C:0.34, G:0.01, T:0.21
Consensus pattern (7 bp):
CTAAACC
Found at i:5234123 original size:23 final size:23
Alignment explanation
Indices: 5234097--5234156 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 23
5234087 CACTAATTAA
**
5234097 TCTAAACCCTAAACCCCTAATTC
1 TCTAAACCCTAAACCCCTAACCC
*
5234120 TCTAAACCCTAAACTCCTAACCC
1 TCTAAACCCTAAACCCCTAACCC
*
5234143 T-TAACCCCTAAACC
1 TCTAAACCCTAAACC
5234157 TTAAACCCCA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
22 11 0.34
23 21 0.66
ACGTcount: A:0.35, C:0.42, G:0.00, T:0.23
Consensus pattern (23 bp):
TCTAAACCCTAAACCCCTAACCC
Found at i:5234852 original size:114 final size:115
Alignment explanation
Indices: 5234647--5234893 Score: 329
Period size: 114 Copynumber: 2.2 Consensus size: 115
5234637 GTCGACCTAT
* *
5234647 AAAAAGCGCCGCTAATGCCACTAAAAGCTCAACATAAAACGACGGTGTTGTGGCTAATTTTTTGC
1 AAAAAGCGCCGCTAATGCCACTAAAAGCTCAACATAAAACAACGGAGTTGTGGCTAATTTTTTGC
* * * * * * *
5234712 GATATTTTTCAATGAGCGCCGCTAATG-TTCGACCTATAGTGGCGTTTTTC
66 GACACTTTTCAAAGAGCGCCGATAATGCTT-GACCTATAGCGACGCTTTTC
*
5234762 AAAAAGCGCCGCTAATTCCACT-AAAGCTCAACATAAAACAACGGAGTTGT-GCTTAATTTTTTG
1 AAAAAGCGCCGCTAATGCCACTAAAAGCTCAACATAAAACAACGGAGTTGTGGC-TAATTTTTTG
* * *
5234825 CGCCGCTTTTCAAAGAGCGCCGATAATGCTTGAGCTATAGCGACGCTTTTC
65 CGACACTTTTCAAAGAGCGCCGATAATGCTTGACCTATAGCGACGCTTTTC
*
5234876 GAAAAGCGCCGCTAATGC
1 AAAAAGCGCCGCTAATGC
5234894 TCAACCTATA
Statistics
Matches: 115, Mismatches: 15, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
113 2 0.02
114 90 0.78
115 23 0.20
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.28
Consensus pattern (115 bp):
AAAAAGCGCCGCTAATGCCACTAAAAGCTCAACATAAAACAACGGAGTTGTGGCTAATTTTTTGC
GACACTTTTCAAAGAGCGCCGATAATGCTTGACCTATAGCGACGCTTTTC
Found at i:5234903 original size:40 final size:39
Alignment explanation
Indices: 5234828--5234933 Score: 122
Period size: 40 Copynumber: 2.6 Consensus size: 39
5234818 TTTTTTGCGC
* ** * *
5234828 CGCTTTTCAAAGAGCGCCGATAATGCTTGAGCTATAGCGA
1 CGCTTTTCAAA-AGCGCCGCTAATGCTCAACCTATAGAGA
*
5234868 CGCTTTTCGAAAAGCGCCGCTAATGCTCAACCTATAGAGG
1 CGCTTTTC-AAAAGCGCCGCTAATGCTCAACCTATAGAGA
*
5234908 CACTTTTCAACAAGCGCCGCTAATGC
1 CGCTTTTCAA-AAGCGCCGCTAATGC
5234934 CACTAAAGCT
Statistics
Matches: 57, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
39 2 0.04
40 52 0.91
41 3 0.05
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (39 bp):
CGCTTTTCAAAAGCGCCGCTAATGCTCAACCTATAGAGA
Found at i:5235045 original size:40 final size:40
Alignment explanation
Indices: 5234985--5235068 Score: 116
Period size: 40 Copynumber: 2.1 Consensus size: 40
5234975 TTTGCTGCGC
* * *
5234985 TTTTCAAAGAGCGCCGCTAATGCTCGACCTATAGCGGCGT
1 TTTTCAAAGAGCGCCACTAATGCCCGACCTATAGCGGCAT
*
5235025 TTTTCAACA-AGCGCCACTAATGCCCGAGCTATAGCGGCAT
1 TTTTCAA-AGAGCGCCACTAATGCCCGACCTATAGCGGCAT
5235065 TTTT
1 TTTT
5235069 TGTCAAAACT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
40 38 0.97
41 1 0.03
ACGTcount: A:0.24, C:0.27, G:0.21, T:0.27
Consensus pattern (40 bp):
TTTTCAAAGAGCGCCACTAATGCCCGACCTATAGCGGCAT
Found at i:5235057 original size:154 final size:153
Alignment explanation
Indices: 5234716--5235068 Score: 476
Period size: 154 Copynumber: 2.3 Consensus size: 153
5234706 TTTTGCGATA
* * * * *
5234716 TTTTTCAATGAGCGCCGCTAATGTTCGACCTATAGTGGCGTTTTTCAAAAAGCGCCGCTAATTCC
1 TTTTTCAA-AAGCGCCGCTAATGCTCGACCTATAGAGGCATTTTTCAAAAAGCGCCGCTAATGCC
*
5234781 ACTAAAGCTCAACATAAAACAACGGAGTTGTGCTTAATTTTTTGCGCCGCTTTTCAAAGAGCGCC
65 ACTAAAGCTCAACATAAAACAACGCAGTTGTGCTTAATTTTTTGCGCCGCTTTTCAAAGAGCGCC
* *
5234846 GATAATGCTTGAGCTATAGCGACG
130 GATAATGCTCGACCTATAGCGACG
* * * *
5234870 CTTTTCGAAAAGCGCCGCTAATGCTCAACCTATAGAGGCACTTTTCAACAAGCGCCGCTAATGCC
1 TTTTTC-AAAAGCGCCGCTAATGCTCGACCTATAGAGGCATTTTTCAAAAAGCGCCGCTAATGCC
*
5234935 ACTAAAGCTCAACATAAAACGACAGCA-TTGTGCTTAATTTTTTGCTG-CGCTTTTCAAAGAGCG
65 ACTAAAGCTCAACATAAAACAAC-GCAGTTGTGCTTAATTTTTTGC-GCCGCTTTTCAAAGAGCG
* *
5234998 CCGCTAATGCTCGACCTATAGCGGCG
128 CCGATAATGCTCGACCTATAGCGACG
* * * *
5235024 TTTTTCAACAAGCGCCACTAATGCCCGAGCTATAGCGGCATTTTT
1 TTTTTCAA-AAGCGCCGCTAATGCTCGACCTATAGAGGCATTTTT
5235069 TGTCAAAACT
Statistics
Matches: 173, Mismatches: 22, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
153 2 0.01
154 166 0.96
155 5 0.03
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.28
Consensus pattern (153 bp):
TTTTTCAAAAGCGCCGCTAATGCTCGACCTATAGAGGCATTTTTCAAAAAGCGCCGCTAATGCCA
CTAAAGCTCAACATAAAACAACGCAGTTGTGCTTAATTTTTTGCGCCGCTTTTCAAAGAGCGCCG
ATAATGCTCGACCTATAGCGACG
Found at i:5237531 original size:18 final size:18
Alignment explanation
Indices: 5237505--5237546 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
5237495 GATTGGGAAA
* *
5237505 AGGAAACATATAAAGGTT
1 AGGATACATATAAAGGCT
*
5237523 AGGATACATATAAGGGCT
1 AGGATACATATAAAGGCT
5237541 AGGATA
1 AGGATA
5237547 TGCACCTGGC
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:0.45, C:0.07, G:0.26, T:0.21
Consensus pattern (18 bp):
AGGATACATATAAAGGCT
Found at i:5241244 original size:3 final size:3
Alignment explanation
Indices: 5241230--5241272 Score: 50
Period size: 3 Copynumber: 14.3 Consensus size: 3
5241220 AAATTGTTAT
* * * *
5241230 TTA TTA TCA TTA TTA TTA TTT TTA TTA TTA TTT TTA TTT TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
5241273 ATTCATGCGC
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (3 bp):
TTA
Found at i:5241261 original size:12 final size:12
Alignment explanation
Indices: 5241239--5241272 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
5241229 TTTATTATCA
5241239 TTATTATTATTT
1 TTATTATTATTT
5241251 TTATTATTATTT
1 TTATTATTATTT
*
5241263 TTATTTTTAT
1 TTATTATTAT
5241273 ATTCATGCGC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (12 bp):
TTATTATTATTT
Found at i:5241539 original size:24 final size:23
Alignment explanation
Indices: 5241491--5241540 Score: 57
Period size: 22 Copynumber: 2.1 Consensus size: 23
5241481 TATATTTTTA
* *
5241491 TATTTTTCTTATGTTCATAAGTG
1 TATTTTTCTTATATTCATAAATG
5241514 TATTTTT-TTATATTCATATTAATG
1 TATTTTTCTTATATTCATA--AATG
5241538 TAT
1 TAT
5241541 ATATTTTGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 10 0.43
23 7 0.30
24 6 0.26
ACGTcount: A:0.26, C:0.06, G:0.08, T:0.60
Consensus pattern (23 bp):
TATTTTTCTTATATTCATAAATG
Found at i:5241742 original size:15 final size:15
Alignment explanation
Indices: 5241719--5241751 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
5241709 GTGATATGTC
5241719 ATTGATGTATTTATT
1 ATTGATGTATTTATT
*
5241734 ATTGTTGTATTTATT
1 ATTGATGTATTTATT
5241749 ATT
1 ATT
5241752 ATAGCATTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.12, T:0.64
Consensus pattern (15 bp):
ATTGATGTATTTATT
Found at i:5246570 original size:54 final size:54
Alignment explanation
Indices: 5246488--5246600 Score: 217
Period size: 54 Copynumber: 2.1 Consensus size: 54
5246478 TTTTTTTTTG
5246488 AATTTGTTATTTTTTGGAATACCTCATTCTTTTCCAAGATATACATTCCCAATC
1 AATTTGTTATTTTTTGGAATACCTCATTCTTTTCCAAGATATACATTCCCAATC
*
5246542 AATTTTTTATTTTTTGGAATACCTCATTCTTTTCCAAGATATACATTCCCAATC
1 AATTTGTTATTTTTTGGAATACCTCATTCTTTTCCAAGATATACATTCCCAATC
5246596 AATTT
1 AATTT
5246601 CTTTGTTATC
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 58 1.00
ACGTcount: A:0.28, C:0.19, G:0.06, T:0.46
Consensus pattern (54 bp):
AATTTGTTATTTTTTGGAATACCTCATTCTTTTCCAAGATATACATTCCCAATC
Found at i:5248104 original size:44 final size:43
Alignment explanation
Indices: 5247621--5248128 Score: 355
Period size: 44 Copynumber: 11.7 Consensus size: 43
5247611 ATCCCATCCT
* *
5247621 CCTGAAGTTGTAGTGGGGCAGACTGAAGATAGCAAGTCTTATC-C
1 CCTGAAGTTGCAGTGGAGCAGACT-AAGA-AGCAAGTCTTATCTC
* *
5247665 TCCTGAAGTTGCAGTGGGGCAGACTGAAGATGGCAAGTCTTATCTC
1 -CCTGAAGTTGCAGTGGAGCAGACT-AAGA-AGCAAGTCTTATCTC
* * *
5247711 CCTGAAGTTGCAGTGGAGCAGA-TTA-AAGCCGATAATCCTATCTC
1 CCTGAAGTTGCAGTGGAGCAGACTAAGAAG-C-A-AGTCTTATCTC
* * * * *
5247755 CCTGAAGTTCCAGTGGAGCGGATTAA-AACCTCAAATCTTATCTC
1 CCTGAAGTTGCAGTGGAGCAGACTAAGAA--GCAAGTCTTATCTC
* * * * * * *
5247799 TCAGAAGTTGCAG-AGAGCAGA-T-CGCATCTAGTCTTATCTC
1 CCTGAAGTTGCAGTGGAGCAGACTAAGAAGCAAGTCTTATCTC
* *
5247839 CCTGAAGTTGCAGTAGAGTAGACTAAGTAAGCAAGTCTTATC-C
1 CCTGAAGTTGCAGTGGAGCAGACTAAG-AAGCAAGTCTTATCTC
* * *
5247882 TCCTGAAGTTGTAGTGGGGCAGACTGAAGATGGCAAGTCTTATCTC
1 -CCTGAAGTTGCAGTGGAGCAGACT-AAGA-AGCAAGTCTTATCTC
* * *
5247928 CCTGAAGTTGCAGTGGAGCAGA-TTA-AAGCCGATAATCCTATCTC
1 CCTGAAGTTGCAGTGGAGCAGACTAAGAAG-C-A-AGTCTTATCTC
* * * *
5247972 CCTGAAGTTGCAGTGGAGCGGATTAA-AACCTCAGATCTTATCTC
1 CCTGAAGTTGCAGTGGAGCAGACTAAGAAGC-AAG-TCTTATCTC
* * * * * * *
5248016 TCTGAAGTTGCAG-AGAGAAGA-T-CGCATCTAGTCTTATCTC
1 CCTGAAGTTGCAGTGGAGCAGACTAAGAAGCAAGTCTTATCTC
5248056 CCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATC-C
1 CCTGAAGTTGCAGTGGAGCAGACTAAG-AAGCAAGTCTTATCTC
5248099 TCCTGAAGTTGCAGT-GAGGCAGACTGAAGA
1 -CCTGAAGTTGCAGTGGA-GCAGACT-AAGA
5248129 TTTCAGATCT
Statistics
Matches: 373, Mismatches: 61, Indels: 59
0.76 0.12 0.12
Matches are distributed among these distances:
40 44 0.12
41 17 0.05
42 11 0.03
43 22 0.06
44 167 0.45
45 109 0.29
46 3 0.01
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.26
Consensus pattern (43 bp):
CCTGAAGTTGCAGTGGAGCAGACTAAGAAGCAAGTCTTATCTC
Found at i:5248192 original size:217 final size:217
Alignment explanation
Indices: 5247482--5248166 Score: 1018
Period size: 217 Copynumber: 3.2 Consensus size: 217
5247472 GGAGCAAATC
* * * *
5247482 GAAGATGGCAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAAATTAAAGCCGATAATCCTATCCC
1 GAAGATGGCAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCTC
* * * * ** *
5247547 CCTGAAGTTGCAGTGGAGCAGATCACAACATTGGATCTTATCTCTTTGAAGTTGCAGAGAGCAGA
66 CCTGAAGTTGCAGTGGAGCGGATTAAAACCTCAGATCTTATCTCTCTGAAGTTGCAGAGAGCAGA
* *
5247612 TC-C--C-A-TC----CT-CCTGAAGTTGTAGTGGGGCAGACTGAAG-ATAGCAAGTCTTATCCT
131 TCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-AAGTA-AGCAAGTCTTATCCT
5247666 CCTGAAGTTGCAGTGGGGCAGACT
194 CCTGAAGTTGCAGTGGGGCAGACT
5247690 GAAGATGGCAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCTC
1 GAAGATGGCAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCTC
* * *
5247755 CCTGAAGTTCCAGTGGAGCGGATTAAAACCTCAAATCTTATCTCTCAGAAGTTGCAGAGAGCAGA
66 CCTGAAGTTGCAGTGGAGCGGATTAAAACCTCAGATCTTATCTCTCTGAAGTTGCAGAGAGCAGA
* *
5247820 TCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTAGAGTAGACTAAGTAAGCAAGTCTTATCCTCC
131 TCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCCTCC
*
5247885 TGAAGTTGTAGTGGGGCAGACT
196 TGAAGTTGCAGTGGGGCAGACT
5247907 GAAGATGGCAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCTC
1 GAAGATGGCAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCTC
*
5247972 CCTGAAGTTGCAGTGGAGCGGATTAAAACCTCAGATCTTATCTCTCTGAAGTTGCAGAGAGAAGA
66 CCTGAAGTTGCAGTGGAGCGGATTAAAACCTCAGATCTTATCTCTCTGAAGTTGCAGAGAGCAGA
5248037 TCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCCTCC
131 TCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCCTCC
*
5248102 TGAAGTTGCAGTGAGGCAGACT
196 TGAAGTTGCAGTGGGGCAGACT
** ** *
5248124 GAAGATTTC-AGATCTTATCTCCCT-AAGCAGTAGTGGAGCAGAT
1 GAAGATGGCAAG-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGAT
5248167 CGAAGATGGT
Statistics
Matches: 433, Mismatches: 32, Indels: 16
0.90 0.07 0.03
Matches are distributed among these distances:
208 118 0.27
209 1 0.00
211 1 0.00
212 1 0.00
213 2 0.00
216 18 0.04
217 271 0.63
218 21 0.05
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.26
Consensus pattern (217 bp):
GAAGATGGCAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCTC
CCTGAAGTTGCAGTGGAGCGGATTAAAACCTCAGATCTTATCTCTCTGAAGTTGCAGAGAGCAGA
TCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCCTCC
TGAAGTTGCAGTGGGGCAGACT
Found at i:5249225 original size:98 final size:98
Alignment explanation
Indices: 5249111--5249993 Score: 1748
Period size: 98 Copynumber: 9.0 Consensus size: 98
5249101 TTAAAAATAA
* *
5249111 TAAAGGAAATATTCCGAGTTTGGGATTTTAAAGGAATTGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
5249176 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
5249209 TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
5249274 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
5249307 TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
5249372 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
5249405 TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
5249470 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
5249503 TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
5249568 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
5249601 TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
5249666 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
5249699 TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
5249764 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
5249797 TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
5249862 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
5249895 TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
5249960 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
5249993 T
1 T
5249994 TATATTGTAC
Statistics
Matches: 783, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
98 783 1.00
ACGTcount: A:0.29, C:0.11, G:0.24, T:0.36
Consensus pattern (98 bp):
TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
Found at i:5251342 original size:85 final size:85
Alignment explanation
Indices: 5251199--5251372 Score: 278
Period size: 85 Copynumber: 2.0 Consensus size: 85
5251189 ACCTAAACCT
* *
5251199 GAGAAGAAAACGACAGCAGTAATAACTACTGATGGTGGTCCATCCAAGAGCAGATCAGGATATAC
1 GAGAAGAAAACGACAGCAGTAATAACTACTGATGGTGGTCCATCCAAGAGAAGATCAGGATATAA
5251264 TGAAGATATTAGAGTAATAG
66 TGAAGATATTAGAGTAATAG
* * *
5251284 GAGAAGAACAA-GGCAGCGGTAGTAACTACTGATGGTGGTCCATCCAAGAGAAGATCAGGATATA
1 GAGAAGAA-AACGACAGCAGTAATAACTACTGATGGTGGTCCATCCAAGAGAAGATCAGGATATA
*
5251348 ATGAAGATATTGGAGTAATAG
65 ATGAAGATATTAGAGTAATAG
5251369 GAGA
1 GAGA
5251373 TGGGTCGAGG
Statistics
Matches: 82, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
85 80 0.98
86 2 0.02
ACGTcount: A:0.40, C:0.13, G:0.28, T:0.20
Consensus pattern (85 bp):
GAGAAGAAAACGACAGCAGTAATAACTACTGATGGTGGTCCATCCAAGAGAAGATCAGGATATAA
TGAAGATATTAGAGTAATAG
Found at i:5253354 original size:20 final size:20
Alignment explanation
Indices: 5253329--5253366 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
5253319 AAAGCTATTC
*
5253329 AGAGGCACCGTAGTGCAAAT
1 AGAGGCACCGAAGTGCAAAT
*
5253349 AGAGGCATCGAAGTGCAA
1 AGAGGCACCGAAGTGCAA
5253367 TACTATACAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.18, G:0.32, T:0.13
Consensus pattern (20 bp):
AGAGGCACCGAAGTGCAAAT
Found at i:5263625 original size:50 final size:50
Alignment explanation
Indices: 5263532--5263724 Score: 154
Period size: 50 Copynumber: 3.7 Consensus size: 50
5263522 TTGTACATAC
* * * * * * **
5263532 TGCCAATGTCATATCGCAGATATGGTCATACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATATCGG
* * *
5263582 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATATCGG
* * * * **
5263632 TGCCAACGCCATGTCCTAGACATGGTCTTA-TGTGAGACCTCTCATAACCTCAATAA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAG-GGGACCTCTCAT-A--TC---GG
*
5263688 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA
5263725 TCTCATTCCT
Statistics
Matches: 110, Mismatches: 25, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
49 1 0.01
50 77 0.70
53 1 0.01
56 31 0.28
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATATCGG
Found at i:5268227 original size:25 final size:25
Alignment explanation
Indices: 5268192--5268263 Score: 126
Period size: 25 Copynumber: 2.9 Consensus size: 25
5268182 CAGTCCTATT
*
5268192 TTTACAACTCGTGTGAGCATACTGA
1 TTTACAGCTCGTGTGAGCATACTGA
5268217 TTTACAGCTCGTGTGAGCATACTGA
1 TTTACAGCTCGTGTGAGCATACTGA
*
5268242 TTTACAGCTCGTGTGAGTATAC
1 TTTACAGCTCGTGTGAGCATAC
5268264 ATGTACAAGA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 45 1.00
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.33
Consensus pattern (25 bp):
TTTACAGCTCGTGTGAGCATACTGA
Found at i:5268750 original size:47 final size:48
Alignment explanation
Indices: 5268669--5268762 Score: 136
Period size: 47 Copynumber: 2.0 Consensus size: 48
5268659 TTAGATGCTT
* * *
5268669 ACTCTGTGTTATTTTTTCGTGTTTTATAGCGAATCAGAAGCTTGTTCA
1 ACTCTGTGTTATTTTTTCATGTTTGATAGCGAATCAGAAGCTCGTTCA
* *
5268717 ACTCTGTTTTA-TTTTTCATGTTTGATAGTGAATCAGAAGCTCGTTC
1 ACTCTGTGTTATTTTTTCATGTTTGATAGCGAATCAGAAGCTCGTTC
5268763 GGGTTGGAAG
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
47 31 0.76
48 10 0.24
ACGTcount: A:0.21, C:0.15, G:0.18, T:0.46
Consensus pattern (48 bp):
ACTCTGTGTTATTTTTTCATGTTTGATAGCGAATCAGAAGCTCGTTCA
Found at i:5269512 original size:30 final size:30
Alignment explanation
Indices: 5269445--5269512 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 30
5269435 TGTGTCTCAC
* *
5269445 CCGTGTGTGACACACGGCCAGGCAACATGG
1 CCGTGTGTGACACACAGCCAGGCAACACGG
* * *
5269475 CCATGTGTGACACACAGCCAGGTAATACGG
1 CCGTGTGTGACACACAGCCAGGCAACACGG
*
5269505 CTGTGTGT
1 CCGTGTGT
5269513 CCCCTATAGC
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.24, C:0.26, G:0.31, T:0.19
Consensus pattern (30 bp):
CCGTGTGTGACACACAGCCAGGCAACACGG
Found at i:5275549 original size:27 final size:28
Alignment explanation
Indices: 5275519--5275578 Score: 81
Period size: 27 Copynumber: 2.2 Consensus size: 28
5275509 TTGAATTCAG
*
5275519 TAAACAACA-GATAG-TCCTCTGGGACAA
1 TAAACAACAGGATAGTTCATC-GGGACAA
5275546 TAAAC-ACAGGATAGTTCATCGGGACAA
1 TAAACAACAGGATAGTTCATCGGGACAA
5275573 TAAACA
1 TAAACA
5275579 CAAGAGAGCC
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
26 3 0.10
27 22 0.76
28 4 0.14
ACGTcount: A:0.43, C:0.20, G:0.18, T:0.18
Consensus pattern (28 bp):
TAAACAACAGGATAGTTCATCGGGACAA
Found at i:5275595 original size:27 final size:27
Alignment explanation
Indices: 5275539--5275613 Score: 87
Period size: 27 Copynumber: 2.8 Consensus size: 27
5275529 ATAGTCCTCT
* * ** *
5275539 GGGACAATAAACACAGGATAGTTCATC
1 GGGACAATAAACACAAGAGAGCCCACC
5275566 GGGACAATAAACACAAGAGAGCCCACC
1 GGGACAATAAACACAAGAGAGCCCACC
* *
5275593 GGGACAGTAAACACGAGAGAG
1 GGGACAATAAACACAAGAGAG
5275614 TTCGCCAATA
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.43, C:0.21, G:0.27, T:0.09
Consensus pattern (27 bp):
GGGACAATAAACACAAGAGAGCCCACC
Found at i:5277533 original size:25 final size:25
Alignment explanation
Indices: 5277472--5277535 Score: 65
Period size: 25 Copynumber: 2.6 Consensus size: 25
5277462 AACCTATTTT
* * *
5277472 ACAGCTTGCGTGAGCATTTACAGTT
1 ACAGCTTGTGTGAGCATTTACACTC
** * *
5277497 ACAGCTCATGTGAGCTTTTACCCTC
1 ACAGCTTGTGTGAGCATTTACACTC
5277522 ACAGCTTGTGTGAG
1 ACAGCTTGTGTGAG
5277536 AATTGTTCCT
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.22, C:0.23, G:0.23, T:0.31
Consensus pattern (25 bp):
ACAGCTTGTGTGAGCATTTACACTC
Found at i:5277614 original size:13 final size:13
Alignment explanation
Indices: 5277583--5277630 Score: 60
Period size: 13 Copynumber: 3.5 Consensus size: 13
5277573 TCATCAGGTG
5277583 GAAATGGATATATAT
1 GAAATGG-T-TATAT
*
5277598 GAAATGGTTATAC
1 GAAATGGTTATAT
*
5277611 GAAATGGATATAT
1 GAAATGGTTATAT
5277624 GAAATGG
1 GAAATGG
5277631 ACATTTGAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
13 22 0.73
14 1 0.03
15 7 0.23
ACGTcount: A:0.44, C:0.02, G:0.25, T:0.29
Consensus pattern (13 bp):
GAAATGGTTATAT
Found at i:5277631 original size:13 final size:13
Alignment explanation
Indices: 5277592--5277655 Score: 76
Period size: 13 Copynumber: 4.9 Consensus size: 13
5277582 GGAAATGGAT
5277592 ATATATGAAATGG
1 ATATATGAAATGG
* *
5277605 TTATACGAAATGG
1 ATATATGAAATGG
5277618 ATATATGAAATGG
1 ATATATGAAATGG
* *
5277631 ACATTTGAAATGG
1 ATATATGAAATGG
5277644 ATACT-TGAAATG
1 ATA-TATGAAATG
5277656 AAAATGTGAA
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
13 42 0.98
14 1 0.02
ACGTcount: A:0.42, C:0.05, G:0.22, T:0.31
Consensus pattern (13 bp):
ATATATGAAATGG
Found at i:5277640 original size:26 final size:26
Alignment explanation
Indices: 5277583--5277655 Score: 76
Period size: 26 Copynumber: 2.7 Consensus size: 26
5277573 TCATCAGGTG
**
5277583 GAAATGGATATATATGAAATGGTTATAC
1 GAAATGG--ATATATGAAATGGACATAC
**
5277611 GAAATGGATATATGAAATGGACATTT
1 GAAATGGATATATGAAATGGACATAC
5277637 GAAATGGATACT-TGAAATG
1 GAAATGGATA-TATGAAATG
5277656 AAAATGTGAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
26 32 0.80
27 1 0.03
28 7 0.17
ACGTcount: A:0.42, C:0.04, G:0.23, T:0.30
Consensus pattern (26 bp):
GAAATGGATATATGAAATGGACATAC
Found at i:5277665 original size:26 final size:26
Alignment explanation
Indices: 5277611--5277666 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
5277601 ATGGTTATAC
* * *
5277611 GAAATGGATATATGAAATGGACATTT
1 GAAATGGATATATGAAATGAAAATGT
5277637 GAAATGGATACT-TGAAATGAAAATGT
1 GAAATGGATA-TATGAAATGAAAATGT
5277663 GAAA
1 GAAA
5277667 AGTTAAATGG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 25 0.96
27 1 0.04
ACGTcount: A:0.46, C:0.04, G:0.23, T:0.27
Consensus pattern (26 bp):
GAAATGGATATATGAAATGAAAATGT
Found at i:5293242 original size:100 final size:99
Alignment explanation
Indices: 5293138--5293827 Score: 710
Period size: 100 Copynumber: 6.9 Consensus size: 99
5293128 TAACTCGTAA
* ** * * * * * * *
5293138 CTTTAATCTGTTTAACTGTGATGTCGAGGAAGTAAGGTTCGCCATTATGGCTTCAATCTGTTCCA
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCA-TGTGGCTTTAATCTGCTCCA
* *
5293203 CTACACTGCCT-GGGAAGTAAGATTCACTGTTGTAG
65 CTGCA-TGCCTAGAGAAGTAAGATTCACTGTTGTAG
* * * * * * * *
5293238 CTTTAATCTTTCTAACTGCAATATCGGGGAAGCGAGATTCGCCGTTGTGGCGTTAATCTGTTTCA
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACC-ATGTGGCTTTAATCTGCTCCA
* * * *
5293303 TTGCA-CCGCTTGAGAGGTAAGATTCACTGTTGTAG
65 CTGCATGC-CTAGAGAAGTAAGATTCACTGTTGTAG
* * *
5293338 CTTTAATCTTTTTAACTGCAATGTCGAGGAAGCAAGGTTCGCCATCGTGGCTTTAATCTGCTCCA
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCAT-GTGGCTTTAATCTGCTCCA
* *
5293403 CTGCAT-CGCTAGAGATGTAAGATTCACTGTTGTGG
65 CTGCATGC-CTAGAGAAGTAAGATTCACTGTTGTAG
* * * * *
5293438 CTTCAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTTAACGATGTGGCTTTAATTTGTTCCA
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGA-TTCACCATGTGGCTTTAATCTGCTCCA
* ** * * ** * *
5293503 CTGTACCACCTGGGGAA-TAAGATTTGCCGTTATAG
65 CTGCA-TGCCTAGAGAAGTAAGATTCACTGTTGTAG
*
5293538 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCGAGATTCACCGATGTGGCTTTAATCTGCTCCA
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACC-ATGTGGCTTTAATCTGCTCCA
* * *
5293603 CTGCAT-CGCTAGAGAAGTAAGATTCACCGCTGTGG
65 CTGCATGC-CTAGAGAAGTAAGATTCACTGTTGTAG
* * *
5293638 CTTTAATCTTTTTAACTACAATGTCAGGGAAGCAAGATTCACCGATGTGGCTTTAATCTACTCCA
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACC-ATGTGGCTTTAATCTGCTCCA
* *
5293703 CTGCATCGCC-AGGGAGGTAAGATTCACTGTTGTAG
65 CTGCAT-GCCTAGAGAAGTAAGATTCACTGTTGTAG
* *
5293738 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCGAGATTCACCGATGTGGCTTTAATCTGCTCTA
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACC-ATGTGGCTTTAATCTGCTCCA
*
5293803 CTGCAT-CTCCAGAGAAGTAAGATTC
65 CTGCATGC-CTAGAGAAGTAAGATTC
5293828 TTGATTTCAC
Statistics
Matches: 494, Mismatches: 81, Indels: 30
0.82 0.13 0.05
Matches are distributed among these distances:
98 3 0.01
99 14 0.03
100 464 0.94
101 11 0.02
102 2 0.00
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Consensus pattern (99 bp):
CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCATGTGGCTTTAATCTGCTCCAC
TGCATGCCTAGAGAAGTAAGATTCACTGTTGTAG
Found at i:5293246 original size:50 final size:50
Alignment explanation
Indices: 5293031--5293807 Score: 327
Period size: 50 Copynumber: 15.5 Consensus size: 50
5293021 AAGATTTGCT
* * * *
5293031 GTTGTGGCTTCAATCTGTTCCACTGCACTGCTTGGGAAGTAAGATTC-GC
1 GTTGTGGCTTTAATCTGTTCCACTGCAATGCCTGGGAAGTAAGATTCACC
* * * ** * * * * *
5293080 TTTGTAGCTTTAATCTTTTTAACTGCAATGTC-GGGGAGATAGGATTTGTAAC
1 GTTGTGGCTTTAATCTGTTCCACTGCAATGCCTGGGAAG-TAAGA-TT-CACC
* ** ** ** * * *
5293132 -TCGTAACTTTAATCTGTTTAACTGTGATGTC-GAGGAAGTAAGGTTCGCC
1 GTTGTGGCTTTAATCTGTTCCACTGCAATGCCTG-GGAAGTAAGATTCACC
* * * * * *
5293181 ATTATGGCTTCAATCTGTTCCACTACACTGCCTGGGAAGTAAGATTCACT
1 GTTGTGGCTTTAATCTGTTCCACTGCAATGCCTGGGAAGTAAGATTCACC
* * ** * ** *
5293231 GTTGTAGCTTTAATCT-TTCTAACTGCAATATCGGGGAAGCGAGATTCGCC
1 GTTGTGGCTTTAATCTGTTC-CACTGCAATGCCTGGGAAGTAAGATTCACC
* * * ** * * * *
5293281 GTTGTGGCGTTAATCTGTTTCATTGCACCGCTTGAGAGGTAAGATTCACT
1 GTTGTGGCTTTAATCTGTTCCACTGCAATGCCTGGGAAGTAAGATTCACC
* * ** * * * *
5293331 GTTGTAGCTTTAATCTTTTTAACTGCAATGTC-GAGGAAGCAAGGTTCGCC
1 GTTGTGGCTTTAATCTGTTCCACTGCAATGCCTG-GGAAGTAAGATTCACC
* * * * * *
5293381 ATCGTGGCTTTAATCTGCTCCACTGC-AT-CGCTAGAGATGTAAGATTCACT
1 GTTGTGGCTTTAATCTGTTCCACTGCAATGC-CT-GGGAAGTAAGATTCACC
* * ** * * * * *
5293431 GTTGTGGCTTCAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTTAAC
1 GTTGTGGCTTTAATCTGTTCCACTGCAATGCCTGGGAAGTAAGATTCACC
* * * *** **
5293481 GATGTGGCTTTAATTTGTTCCACTGTACCACCTGGGGAA-TAAGATTTGCC
1 GTTGTGGCTTTAATCTGTTCCACTGCAATGCCT-GGGAAGTAAGATTCACC
* * * ** * * **
5293531 GTTATAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCGAGATTCACC
1 GTTGTGGCTTTAATCTGTTCCACTGCAATGCCTGGGAAGTAAGATTCACC
* * *
5293581 GATGTGGCTTTAATCTGCTCCACTGC-AT-CGCTAGAGAAGTAAGATTCACC
1 GTTGTGGCTTTAATCTGTTCCACTGCAATGC-CT-GGGAAGTAAGATTCACC
* * ** * * * *
5293631 GCTGTGGCTTTAATCTTTTTAACTACAATGTCAGGGAAGCAAGATTCACC
1 GTTGTGGCTTTAATCTGTTCCACTGCAATGCCTGGGAAGTAAGATTCACC
* ** * * *
5293681 GATGTGGCTTTAATCTACTCCACTGC-ATCGCCAGGGAGGTAAGATTCACT
1 GTTGTGGCTTTAATCTGTTCCACTGCAAT-GCCTGGGAAGTAAGATTCACC
* * ** * * **
5293731 GTTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCGAGATTCACC
1 GTTGTGGCTTTAATCTGTTCCACTGCAATGCCTGGGAAGTAAGATTCACC
* * *
5293781 GATGTGGCTTTAATCTGCTCTACTGCA
1 GTTGTGGCTTTAATCTGTTCCACTGCA
5293808 TCTCCAGAGA
Statistics
Matches: 509, Mismatches: 196, Indels: 45
0.68 0.26 0.06
Matches are distributed among these distances:
48 5 0.01
49 45 0.09
50 407 0.80
51 47 0.09
52 5 0.01
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Consensus pattern (50 bp):
GTTGTGGCTTTAATCTGTTCCACTGCAATGCCTGGGAAGTAAGATTCACC
Found at i:5293377 original size:200 final size:199
Alignment explanation
Indices: 5293138--5293827 Score: 823
Period size: 200 Copynumber: 3.5 Consensus size: 199
5293128 TAACTCGTAA
* ** * * * *
5293138 CTTTAATCTGTTTAACTGTGATGTCGAGGAAGTAAGGTTCGCCATTATGGCTTCAATCTGTTCCA
1 CTTTAATCTTTTTAACTGCAATGTCGAGGAAGCAAGGTTCGCCATTGTGGCTTTAATCTGCTCCA
* * * * *
5293203 CTACA-CTGCCT-GGGAAGTAAGATTCACTGTTGTAGCTTTAATCTTTCTAACTGCAATATCGGG
66 CTGCATC-G-CTAGAGAAGTAAGATTCACTGTTGTGGCTTTAATCTTTTTAACTGCAATGTCGGG
* * * * * * *
5293266 GAAGCGAGATTCGCCGTTGTGGCGTTAATCTGTTTCATTGCACCGCTTGAGAGGTAAGATTCACT
129 GAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCACTGCACCGCCTG-GAGGTAAGATTCACT
5293331 GTTGTAG
193 GTTGTAG
*
5293338 CTTTAATCTTTTTAACTGCAATGTCGAGGAAGCAAGGTTCGCCATCGTGGCTTTAATCTGCTCCA
1 CTTTAATCTTTTTAACTGCAATGTCGAGGAAGCAAGGTTCGCCATTGTGGCTTTAATCTGCTCCA
* *
5293403 CTGCATCGCTAGAGATGTAAGATTCACTGTTGTGGCTTCAATCTTTTTAACTGCAATGTCGGGGA
66 CTGCATCGCTAGAGAAGTAAGATTCACTGTTGTGGCTTTAATCTTTTTAACTGCAATGTCGGGGA
* * * * * ** *
5293468 AGCAAGATTTAACGATGTGGCTTTAATTTGTTCCACTGTACCACCTGG-GGAATAAGATTTGCCG
131 AGCAAGATTCACCGATGTGGCTTTAATCTGTTCCACTGCACCGCCTGGAGG--TAAGATTCACTG
*
5293532 TTATAG
194 TTGTAG
* * * *
5293538 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCGAGATTCACCGA-TGTGGCTTTAATCTGCTCC
1 CTTTAATCTTTTTAACTGCAATGTCGAGGAAGCAAGGTTCGCC-ATTGTGGCTTTAATCTGCTCC
* * * *
5293602 ACTGCATCGCTAGAGAAGTAAGATTCACCGCTGTGGCTTTAATCTTTTTAACTACAATGTCAGGG
65 ACTGCATCGCTAGAGAAGTAAGATTCACTGTTGTGGCTTTAATCTTTTTAACTGCAATGTCGGGG
** * *
5293667 AAGCAAGATTCACCGATGTGGCTTTAATCTACTCCACTGCATCGCCAGGGAGGTAAGATTCACTG
130 AAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCACTGCACCGCC-TGGAGGTAAGATTCACTG
5293732 TTGTAG
194 TTGTAG
* * * * *
5293738 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCGAGATTCACCGA-TGTGGCTTTAATCTGCTCT
1 CTTTAATCTTTTTAACTGCAATGTCGAGGAAGCAAGGTTCGCC-ATTGTGGCTTTAATCTGCTCC
* *
5293802 ACTGCATCTCCAGAGAAGTAAGATTC
65 ACTGCATCGCTAGAGAAGTAAGATTC
5293828 TTGATTTCAC
Statistics
Matches: 425, Mismatches: 58, Indels: 14
0.86 0.12 0.03
Matches are distributed among these distances:
198 2 0.00
199 3 0.01
200 414 0.97
201 4 0.01
202 2 0.00
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Consensus pattern (199 bp):
CTTTAATCTTTTTAACTGCAATGTCGAGGAAGCAAGGTTCGCCATTGTGGCTTTAATCTGCTCCA
CTGCATCGCTAGAGAAGTAAGATTCACTGTTGTGGCTTTAATCTTTTTAACTGCAATGTCGGGGA
AGCAAGATTCACCGATGTGGCTTTAATCTGTTCCACTGCACCGCCTGGAGGTAAGATTCACTGTT
GTAG
Found at i:5293996 original size:10 final size:9
Alignment explanation
Indices: 5293966--5293995 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
5293956 GAATGCAGAA
5293966 TTTTA-TTT
1 TTTTATTTT
5293974 TTTTATTTT
1 TTTTATTTT
5293983 TTTTATTTT
1 TTTTATTTT
5293992 TTTT
1 TTTT
5293996 TGAGAATGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 5 0.24
9 16 0.76
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (9 bp):
TTTTATTTT
Found at i:5295118 original size:22 final size:21
Alignment explanation
Indices: 5295093--5295134 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
5295083 TTAGCCTCTC
* *
5295093 CATTTTTACTTTTTCTTTTTTT
1 CATTTTT-CATTTTCATTTTTT
5295115 CATTTTTCATTTTCATTTTT
1 CATTTTTCATTTTCATTTTT
5295135 CATCCCCCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.12, C:0.14, G:0.00, T:0.74
Consensus pattern (21 bp):
CATTTTTCATTTTCATTTTTT
Found at i:5295127 original size:13 final size:13
Alignment explanation
Indices: 5295111--5295137 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5295101 CTTTTTCTTT
5295111 TTTTCATTTTTCA
1 TTTTCATTTTTCA
5295124 TTTTCATTTTTCA
1 TTTTCATTTTTCA
5295137 T
1 T
5295138 CCCCCATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTTCATTTTTCA
Found at i:5296054 original size:12 final size:12
Alignment explanation
Indices: 5296037--5296104 Score: 59
Period size: 12 Copynumber: 5.8 Consensus size: 12
5296027 TTTTTCCTTT
5296037 TTTTGATTTTGA
1 TTTTGATTTTGA
*
5296049 TTTTGACTTTGA
1 TTTTGATTTTGA
**
5296061 TTTTTCTTTT--
1 TTTTGATTTTGA
** *
5296071 TTTTTCTTTTTA
1 TTTTGATTTTGA
*
5296083 TTTTGATTTTCA
1 TTTTGATTTTGA
5296095 TTTTGATTTT
1 TTTTGATTTT
5296105 TTTTATTTTT
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
10 10 0.21
12 37 0.79
ACGTcount: A:0.12, C:0.06, G:0.09, T:0.74
Consensus pattern (12 bp):
TTTTGATTTTGA
Found at i:5296060 original size:34 final size:34
Alignment explanation
Indices: 5296022--5296098 Score: 100
Period size: 34 Copynumber: 2.3 Consensus size: 34
5296012 CCTTTTTTAT
5296022 TTTGATTTTTCCTTTTTTTGATTTTGATTTTGAC
1 TTTGATTTTTCCTTTTTTTGATTTTGATTTTGAC
* ** * *
5296056 TTTGATTTTTCTTTTTTTTTCTTTTTATTTTGAT
1 TTTGATTTTTCCTTTTTTTGATTTTGATTTTGAC
*
5296090 TTTCATTTT
1 TTTGATTTT
5296099 GATTTTTTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.10, C:0.08, G:0.08, T:0.74
Consensus pattern (34 bp):
TTTGATTTTTCCTTTTTTTGATTTTGATTTTGAC
Found at i:5296086 original size:40 final size:42
Alignment explanation
Indices: 5296036--5296116 Score: 121
Period size: 40 Copynumber: 2.0 Consensus size: 42
5296026 ATTTTTCCTT
*
5296036 TTTTTGATTTTGATTTTGACTTTGATTTTTCTT-TTTTTTTC
1 TTTTTGATTTTGATTTTCACTTTGATTTTTCTTATTTTTTTC
* *
5296077 TTTTT-ATTTTGATTTTCATTTTGATTTTTTTTATTTTTTT
1 TTTTTGATTTTGATTTTCACTTTGATTTTTCTTATTTTTTT
5296117 TATTTTTGGA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
40 24 0.67
41 12 0.33
ACGTcount: A:0.11, C:0.05, G:0.07, T:0.77
Consensus pattern (42 bp):
TTTTTGATTTTGATTTTCACTTTGATTTTTCTTATTTTTTTC
Found at i:5296113 original size:8 final size:9
Alignment explanation
Indices: 5296060--5296123 Score: 51
Period size: 9 Copynumber: 6.7 Consensus size: 9
5296050 TTTGACTTTG
5296060 ATTTTTCTTT
1 ATTTTT-TTT
5296070 -TTTTTTCTT
1 ATTTTTT-TT
*
5296079 -TTTATTTTG
1 ATTT-TTTTT
5296088 ATTTTCATTTT
1 ATTTT--TTTT
5296099 GATTTTTTTT
1 -ATTTTTTTT
5296109 ATTTTTTTT
1 ATTTTTTTT
5296118 ATTTTT
1 ATTTTT
5296124 GGATTGGATC
Statistics
Matches: 46, Mismatches: 2, Indels: 13
0.75 0.03 0.21
Matches are distributed among these distances:
8 1 0.02
9 27 0.59
10 10 0.22
11 3 0.07
12 5 0.11
ACGTcount: A:0.11, C:0.05, G:0.03, T:0.81
Consensus pattern (9 bp):
ATTTTTTTT
Found at i:5301594 original size:16 final size:16
Alignment explanation
Indices: 5301573--5301605 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
5301563 TTTAAAAGAT
5301573 TTGAAA-GAAAACTCAA
1 TTGAAATGAAAA-TCAA
5301589 TTGAAATGAAAATCAA
1 TTGAAATGAAAATCAA
5301605 T
1 T
5301606 GTCGAAGGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.55, C:0.09, G:0.12, T:0.24
Consensus pattern (16 bp):
TTGAAATGAAAATCAA
Found at i:5303410 original size:21 final size:21
Alignment explanation
Indices: 5303384--5303425 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
5303374 CCACAGCTCG
*
5303384 AAAGAGTGTCCCGTTATTAGC
1 AAAGAGTGTCCCGTCATTAGC
5303405 AAAGAGTGTCCCGTCATTAGC
1 AAAGAGTGTCCCGTCATTAGC
5303426 TCTAATGAGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (21 bp):
AAAGAGTGTCCCGTCATTAGC
Found at i:5303610 original size:25 final size:24
Alignment explanation
Indices: 5303582--5303648 Score: 71
Period size: 27 Copynumber: 2.6 Consensus size: 24
5303572 CGATATATGG
5303582 CTCTCTGGAGCTTCCCGATTAAAGA
1 CTCTCT-GAGCTTCCCGATTAAAGA
* *
5303607 CTCTTTCATGAGCTTCCCGATTAATGG
1 CTC--TC-TGAGCTTCCCGATTAAAGA
5303634 CTCTCTAGAGCTTCC
1 CTCTCT-GAGCTTCC
5303649 TGATATTGGC
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
24 1 0.03
25 13 0.36
27 21 0.58
28 1 0.03
ACGTcount: A:0.19, C:0.30, G:0.18, T:0.33
Consensus pattern (24 bp):
CTCTCTGAGCTTCCCGATTAAAGA
Found at i:5303707 original size:25 final size:25
Alignment explanation
Indices: 5303678--5303735 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
5303668 CTTCTCGATT
** *
5303678 ATGGCTTTTATGAGCTTCCTGTTAC
1 ATGGCTTACATGAGCTTCCCGTTAC
* *
5303703 ATGGCTCACATGAGCTTCCCGTTAT
1 ATGGCTTACATGAGCTTCCCGTTAC
5303728 ATGGCTTA
1 ATGGCTTA
5303736 AAAGAGAGCT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.19, C:0.22, G:0.21, T:0.38
Consensus pattern (25 bp):
ATGGCTTACATGAGCTTCCCGTTAC
Found at i:5304389 original size:2 final size:2
Alignment explanation
Indices: 5304384--5304412 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5304374 TGATATATAA
5304384 GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
5304413 GCTTTATCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.52, T:0.48
Consensus pattern (2 bp):
GT
Found at i:5305457 original size:25 final size:25
Alignment explanation
Indices: 5305423--5305492 Score: 106
Period size: 25 Copynumber: 2.8 Consensus size: 25
5305413 CAGGCCTATT
5305423 TTCACAGCTCGTGTGAGCATTCTA-A
1 TTCACAGCTCGTGTGAGCATTC-AGA
*
5305448 TTCACAGCTCGTGTGTGCATTCAGA
1 TTCACAGCTCGTGTGAGCATTCAGA
*
5305473 TTTACAGCTCGTGTGAGCAT
1 TTCACAGCTCGTGTGAGCAT
5305493 ATGTAACGCC
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
24 1 0.02
25 40 0.98
ACGTcount: A:0.21, C:0.23, G:0.23, T:0.33
Consensus pattern (25 bp):
TTCACAGCTCGTGTGAGCATTCAGA
Found at i:5307116 original size:17 final size:18
Alignment explanation
Indices: 5307094--5307128 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
5307084 ATTTGGGTCA
5307094 TGTGGG-CCACACGGGTG
1 TGTGGGCCCACACGGGTG
5307111 TGTGGGCCCACACGGGTG
1 TGTGGGCCCACACGGGTG
5307129 AACATCATGG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.11, C:0.26, G:0.46, T:0.17
Consensus pattern (18 bp):
TGTGGGCCCACACGGGTG
Found at i:5307901 original size:15 final size:16
Alignment explanation
Indices: 5307874--5307904 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
5307864 TTAAGTTAAA
5307874 GAAAGTAAATGAAATG
1 GAAAGTAAATGAAATG
5307890 GAAAGT-AATGAAATG
1 GAAAGTAAATGAAATG
5307905 CAAATGAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.55, C:0.00, G:0.26, T:0.19
Consensus pattern (16 bp):
GAAAGTAAATGAAATG
Found at i:5308390 original size:15 final size:16
Alignment explanation
Indices: 5308370--5308399 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5308360 TGGTGCCTTG
5308370 TTGAT-ATGTGTTAAT
1 TTGATAATGTGTTAAT
5308385 TTGATAATGTGTTAA
1 TTGATAATGTGTTAA
5308400 AATATGTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.30, C:0.00, G:0.20, T:0.50
Consensus pattern (16 bp):
TTGATAATGTGTTAAT
Found at i:5310685 original size:138 final size:138
Alignment explanation
Indices: 5310451--5310766 Score: 431
Period size: 138 Copynumber: 2.3 Consensus size: 138
5310441 GCTCCTAGTT
* * * *
5310451 GAAGAGCCGTAGCCTCCAAAATAGTTAGTGAAAGCAAAGCTCCCAATTGTAATATCAAGGCTCAC
1 GAAGAGCCGCAGCCTCCAAAATAGTTAGCGAGAGCAAAGCTCCCAATTGTAAGATCAAGGCTCAC
* * * * *
5310516 AGGTGAAGAGTCGCAGCCTCCAAAACAGTTAGCGA-AAGCAAAGCTCCCAACTGTAATATCAAGG
66 AGGCGAAGAGCCACAGCCTCCAAAACAGTTAGCGAGAA-CAAAGCTCCCAACAGTAATATCAAAG
5310580 CTC-CAAAGC
130 CTCAC-AAGC
* * * *
5310589 GAAGAGCCGCAACCTCCAAAATAGTTAGCGAGAGCAAAGCTCCTAATTGTAAGATCGAGGCTCAT
1 GAAGAGCCGCAGCCTCCAAAATAGTTAGCGAGAGCAAAGCTCCCAATTGTAAGATCAAGGCTCAC
* *
5310654 AGGCGAAGAGCCACAGCCTCCAAAACAGTTAGCGAGAACAAAGCTTCCAGCAGTAATATCAAAGC
66 AGGCGAAGAGCCACAGCCTCCAAAACAGTTAGCGAGAACAAAGCTCCCAACAGTAATATCAAAGC
5310719 TCACAAGC
131 TCACAAGC
* *
5310727 AAAGAGCCGCGGCCTCCAAAATAGTTAGC-ACGAGCAAAGC
1 GAAGAGCCGCAGCCTCCAAAATAGTTAGCGA-GAGCAAAGC
5310767 AACTAGGTGT
Statistics
Matches: 157, Mismatches: 18, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
137 1 0.01
138 153 0.97
139 3 0.02
ACGTcount: A:0.37, C:0.25, G:0.22, T:0.16
Consensus pattern (138 bp):
GAAGAGCCGCAGCCTCCAAAATAGTTAGCGAGAGCAAAGCTCCCAATTGTAAGATCAAGGCTCAC
AGGCGAAGAGCCACAGCCTCCAAAACAGTTAGCGAGAACAAAGCTCCCAACAGTAATATCAAAGC
TCACAAGC
Found at i:5310765 original size:69 final size:69
Alignment explanation
Indices: 5310451--5310766 Score: 375
Period size: 69 Copynumber: 4.6 Consensus size: 69
5310441 GCTCCTAGTT
* * * *
5310451 GAAGAGCCGTAGCCTCCAAAATAGTTAGTGAAAGCAAAGCTCCCAATTGTAATATCAAGGCTCAC
1 GAAGAGCCGCAGCCTCCAAAATAGTTAGCGAGAGCAAAGCTCCCAACTGTAATATCAAGGCTCAC
* *
5310516 AGGT
66 AAGC
* * *
5310520 GAAGAGTCGCAGCCTCCAAAACAGTTAGCGAAAGCAAAGCTCCCAACTGTAATATCAAGGCTC-C
1 GAAGAGCCGCAGCCTCCAAAATAGTTAGCGAGAGCAAAGCTCCCAACTGTAATATCAAGGCTCAC
5310584 AAAGC
66 -AAGC
* * * * * *
5310589 GAAGAGCCGCAACCTCCAAAATAGTTAGCGAGAGCAAAGCTCCTAATTGTAAGATCGAGGCTCAT
1 GAAGAGCCGCAGCCTCCAAAATAGTTAGCGAGAGCAAAGCTCCCAACTGTAATATCAAGGCTCAC
*
5310654 AGGC
66 AAGC
* * * * * * *
5310658 GAAGAGCCACAGCCTCCAAAACAGTTAGCGAGAACAAAGCTTCCAGCAGTAATATCAAAGCTCAC
1 GAAGAGCCGCAGCCTCCAAAATAGTTAGCGAGAGCAAAGCTCCCAACTGTAATATCAAGGCTCAC
5310723 AAGC
66 AAGC
* *
5310727 AAAGAGCCGCGGCCTCCAAAATAGTTAGC-ACGAGCAAAGC
1 GAAGAGCCGCAGCCTCCAAAATAGTTAGCGA-GAGCAAAGC
5310767 AACTAGGTGT
Statistics
Matches: 208, Mismatches: 36, Indels: 6
0.83 0.14 0.02
Matches are distributed among these distances:
68 2 0.01
69 206 0.99
ACGTcount: A:0.37, C:0.25, G:0.22, T:0.16
Consensus pattern (69 bp):
GAAGAGCCGCAGCCTCCAAAATAGTTAGCGAGAGCAAAGCTCCCAACTGTAATATCAAGGCTCAC
AAGC
Found at i:5310907 original size:58 final size:58
Alignment explanation
Indices: 5310812--5310930 Score: 168
Period size: 58 Copynumber: 2.1 Consensus size: 58
5310802 GCAGTATCAA
* *
5310812 TATAGAATAGATCGCGAATTCATATTCCCAGCTTATAATTTTGAGAAAAATATCTAAG
1 TATAAAATAGATCGCGAATTCATATTCCCAGCTTATAATTTCGAGAAAAATATCTAAG
* ** *
5310870 TATAAAATAGAT-GACGAATTTATATTCTTAGCTTATAATTTCGAGAAAAATCTCTAAG
1 TATAAAATAGATCG-CGAATTCATATTCCCAGCTTATAATTTCGAGAAAAATATCTAAG
5310928 TAT
1 TAT
5310931 CAGACAGCTC
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
57 1 0.02
58 53 0.98
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (58 bp):
TATAAAATAGATCGCGAATTCATATTCCCAGCTTATAATTTCGAGAAAAATATCTAAG
Found at i:5313750 original size:12 final size:12
Alignment explanation
Indices: 5313733--5313759 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
5313723 CCAAGACTGA
5313733 GACAAAATGGTG
1 GACAAAATGGTG
5313745 GACAAAATGGTG
1 GACAAAATGGTG
5313757 GAC
1 GAC
5313760 CCAATTACGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.11, G:0.33, T:0.15
Consensus pattern (12 bp):
GACAAAATGGTG
Found at i:5314169 original size:17 final size:17
Alignment explanation
Indices: 5314149--5314199 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 17
5314139 CTTTAATGAT
*
5314149 TTTTATAATTATTTAAG
1 TTTTATAATTATTTAAA
*
5314166 TTTTATGATT-TTTAAA
1 TTTTATAATTATTTAAA
* *
5314182 ATTT-TAATTATTTTAA
1 TTTTATAATTATTTAAA
5314198 TT
1 TT
5314200 ATTTTAAATA
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
15 4 0.15
16 14 0.52
17 9 0.33
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (17 bp):
TTTTATAATTATTTAAA
Found at i:5314194 original size:9 final size:9
Alignment explanation
Indices: 5314182--5314213 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
5314172 GATTTTTAAA
5314182 ATTTTAATT
1 ATTTTAATT
5314191 ATTTTAATT
1 ATTTTAATT
*
5314200 ATTTTAAAT
1 ATTTTAATT
5314209 ATTTT
1 ATTTT
5314214 TCTTATAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (9 bp):
ATTTTAATT
Found at i:5315233 original size:12 final size:12
Alignment explanation
Indices: 5315216--5315259 Score: 61
Period size: 12 Copynumber: 3.6 Consensus size: 12
5315206 AAAGTAAATT
5315216 TAAAAAACTAAAA
1 TAAAAAA-TAAAA
* *
5315229 CAAAAATTAAAA
1 TAAAAAATAAAA
5315241 TAAAAAATAAAA
1 TAAAAAATAAAA
5315253 TAAAAAA
1 TAAAAAA
5315260 CCAAATTATA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
12 22 0.81
13 5 0.19
ACGTcount: A:0.80, C:0.05, G:0.00, T:0.16
Consensus pattern (12 bp):
TAAAAAATAAAA
Found at i:5315595 original size:13 final size:13
Alignment explanation
Indices: 5315577--5315604 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
5315567 AGTATCGCTA
5315577 CAGTATTTAATCT
1 CAGTATTTAATCT
5315590 CAGTATTTAATCT
1 CAGTATTTAATCT
5315603 CA
1 CA
5315605 CAGCCACTGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.18, G:0.07, T:0.43
Consensus pattern (13 bp):
CAGTATTTAATCT
Found at i:5316307 original size:6 final size:6
Alignment explanation
Indices: 5316296--5316322 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
5316286 TCCCCCGTCA
5316296 CTCTCC CTCTCC CTCTCC CTCTCC CTC
1 CTCTCC CTCTCC CTCTCC CTCTCC CTC
5316323 GCTGCTGCTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.67, G:0.00, T:0.33
Consensus pattern (6 bp):
CTCTCC
Found at i:5319746 original size:16 final size:16
Alignment explanation
Indices: 5319725--5319786 Score: 63
Period size: 16 Copynumber: 3.9 Consensus size: 16
5319715 TTAGACAAAA
*
5319725 GAATAGAGTTGTAATG
1 GAATAGAGCTGTAATG
*
5319741 GAATAGGGCTGTAATG
1 GAATAGAGCTGTAATG
* * *
5319757 GAATAAATCTATAATG
1 GAATAGAGCTGTAATG
5319773 GAATTA-AGCTGTAA
1 GAA-TAGAGCTGTAA
5319787 CCAGTAATTC
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
16 35 0.95
17 2 0.05
ACGTcount: A:0.40, C:0.05, G:0.26, T:0.29
Consensus pattern (16 bp):
GAATAGAGCTGTAATG
Found at i:5319994 original size:26 final size:26
Alignment explanation
Indices: 5319946--5319999 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 26
5319936 TTGTTATTAA
* ** * *
5319946 AATTTAATAAAATTACTATTAAATAT
1 AATTTAATAAAAATAAAAATAAAAAT
5319972 AATTTAATAAAAATAAAAATAAAAAT
1 AATTTAATAAAAATAAAAATAAAAAT
5319998 AA
1 AA
5320000 ACAATTTAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (26 bp):
AATTTAATAAAAATAAAAATAAAAAT
Found at i:5331279 original size:20 final size:20
Alignment explanation
Indices: 5331237--5331300 Score: 69
Period size: 20 Copynumber: 3.2 Consensus size: 20
5331227 AGCTAATAAC
*
5331237 GAGCTC-AATGATCTGAA-TT
1 GAGCTCGAATGAGCT-AACTT
**
5331256 GAGCTCGTGTGAGCTAACTT
1 GAGCTCGAATGAGCTAACTT
*
5331276 GAGCTCGAATGAGCTGACTT
1 GAGCTCGAATGAGCTAACTT
5331296 GAGCT
1 GAGCT
5331301 AAAGTGAGCT
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
19 8 0.22
20 29 0.78
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (20 bp):
GAGCTCGAATGAGCTAACTT
Found at i:5331308 original size:20 final size:21
Alignment explanation
Indices: 5331264--5331312 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
5331254 TTGAGCTCGT
* *
5331264 GTGAGCTAACTTGAGCTCGAA
1 GTGAGCTGACTTGAGCTCAAA
5331285 -TGAGCTGACTTGAGCT-AAA
1 GTGAGCTGACTTGAGCTCAAA
5331304 GTGAGCTGA
1 GTGAGCTGA
5331313 ACCCGAATGA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 23 0.92
ACGTcount: A:0.29, C:0.16, G:0.31, T:0.24
Consensus pattern (21 bp):
GTGAGCTGACTTGAGCTCAAA
Found at i:5331330 original size:35 final size:35
Alignment explanation
Indices: 5331281--5331350 Score: 113
Period size: 35 Copynumber: 2.0 Consensus size: 35
5331271 AACTTGAGCT
*
5331281 CGAATGAGCTGACTTGAGCTAAAGTGAGCTGAACC
1 CGAATGAGCAGACTTGAGCTAAAGTGAGCTGAACC
* *
5331316 CGAATGAGCAGACTTGAGCTCAAGTGAGTTGAACC
1 CGAATGAGCAGACTTGAGCTAAAGTGAGCTGAACC
5331351 GCATGGAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.31, C:0.20, G:0.29, T:0.20
Consensus pattern (35 bp):
CGAATGAGCAGACTTGAGCTAAAGTGAGCTGAACC
Found at i:5348017 original size:20 final size:20
Alignment explanation
Indices: 5347994--5348034 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
5347984 TTAAATAAGT
5347994 AATTAAGT-AAATAAAGACAA
1 AATTAAGTAAAATAAAG-CAA
*
5348014 AATTTAGTAAAATAAAGCAA
1 AATTAAGTAAAATAAAGCAA
5348034 A
1 A
5348035 GTATCATCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.63, C:0.05, G:0.10, T:0.22
Consensus pattern (20 bp):
AATTAAGTAAAATAAAGCAA
Found at i:5348861 original size:43 final size:43
Alignment explanation
Indices: 5348800--5348953 Score: 193
Period size: 43 Copynumber: 3.6 Consensus size: 43
5348790 TCCAATATCA
5348800 ATTTGAGATTTCGTGTAAGACCATAGCTAGGCTATTGACATCG
1 ATTTGAGATTTCGTGTAAGACCATAGCTAGGCTATTGACATCG
* * *
5348843 ATTTGAGATTTCGTGTAAGACAATAGCTGGGCTATTGGCATCG
1 ATTTGAGATTTCGTGTAAGACCATAGCTAGGCTATTGACATCG
* ** *
5348886 ATTTGAGATCTCGTGTAAGAATATAACTAGGCTATTGGA-ATCG
1 ATTTGAGATTTCGTGTAAGACCATAGCTAGGCTATT-GACATCG
** *
5348929 ATACGAGATTTCCATGTAAGACCAT
1 ATTTGAGATTT-CGTGTAAGACCAT
5348954 GTCTGGGACA
Statistics
Matches: 94, Mismatches: 15, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
43 83 0.88
44 11 0.12
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.32
Consensus pattern (43 bp):
ATTTGAGATTTCGTGTAAGACCATAGCTAGGCTATTGACATCG
Found at i:5370004 original size:27 final size:26
Alignment explanation
Indices: 5369973--5370100 Score: 107
Period size: 27 Copynumber: 4.8 Consensus size: 26
5369963 ATCTACCCTC
* *
5369973 TAGGGGCATTTCGGTTATTTTACCTT
1 TAGGGGTATTTCGGTAATTTTACCTT
* *
5369999 ATAGGGGTATTTTGGTCATTTTACCCTT
1 -TAGGGGTATTTCGGTAATTTTA-CCTT
* *
5370027 TGGGGGTATTTCGATAATTTTACACTT
1 TAGGGGTATTTCGGTAATTTTAC-CTT
* *
5370054 T-GAGGGTATTTCGATAATTTTACCCAT
1 TAG-GGGTATTTCGGTAATTTTA-CCTT
* *
5370081 AAAGGGTATTT-GGTAATTTT
1 TAGGGGTATTTCGGTAATTTT
5370101 TTGGCCCAAG
Statistics
Matches: 85, Mismatches: 11, Indels: 11
0.79 0.10 0.10
Matches are distributed among these distances:
26 10 0.12
27 70 0.82
28 5 0.06
ACGTcount: A:0.22, C:0.12, G:0.22, T:0.45
Consensus pattern (26 bp):
TAGGGGTATTTCGGTAATTTTACCTT
Found at i:5373452 original size:17 final size:17
Alignment explanation
Indices: 5373420--5373465 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
5373410 TTGAAGTGTC
* *
5373420 TTTTGAAAATCGTGTTT
1 TTTTGAAAACCATGTTT
5373437 TTTTGAAAACCATGTTT
1 TTTTGAAAACCATGTTT
*
5373454 TCATTGAAAACC
1 T-TTTGAAAACC
5373466 CTTCCTGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
17 16 0.64
18 9 0.36
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.43
Consensus pattern (17 bp):
TTTTGAAAACCATGTTT
Done.