Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 97507971
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: 97507971
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 232 characters in sequence are not A, C, G, or T
File 105 of 328
Found at i:29240328 original size:18 final size:18
Alignment explanation
Indices: 29240307--29240395 Score: 55
Period size: 18 Copynumber: 5.2 Consensus size: 18
29240297 TTTTTAATAT
29240307 TATATTATTATTTTTGTA
1 TATATTATTATTTTTGTA
* *
29240325 TATATTATT-TTATT-AA
1 TATATTATTATTTTTGTA
** *
29240341 GCTATT-TGTA-TTTTGTG
1 TATATTAT-TATTTTTGTA
* *
29240358 TATATTATT-TATTCGTA
1 TATATTATTATTTTTGTA
29240375 TATATATATTA-TTTTGTA
1 TATAT-TATTATTTTTGTA
29240393 TAT
1 TAT
29240396 CATTTATACT
Statistics
Matches: 50, Mismatches: 14, Indels: 14
0.64 0.18 0.18
Matches are distributed among these distances:
15 1 0.02
16 9 0.18
17 18 0.36
18 22 0.44
ACGTcount: A:0.28, C:0.02, G:0.08, T:0.62
Consensus pattern (18 bp):
TATATTATTATTTTTGTA
Found at i:29244230 original size:40 final size:39
Alignment explanation
Indices: 29244065--29244248 Score: 138
Period size: 40 Copynumber: 4.6 Consensus size: 39
29244055 AAATTGAATG
* * *
29244065 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAAT--T
1 ATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATCGT
* * * * * *
29244105 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-T
* * * * *
29244145 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATC-GT
*
29244185 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
* * *
29244224 GATATCCGGGTTAAGTCCCGTAGGC
1 -ATATCCGGGCTAAGACCCGAAGGC
29244249 CTTGGTGCGG
Statistics
Matches: 113, Mismatches: 26, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
37 4 0.04
38 2 0.02
39 3 0.03
40 104 0.92
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
Found at i:29244273 original size:80 final size:81
Alignment explanation
Indices: 29244105--29244293 Score: 186
Period size: 80 Copynumber: 2.4 Consensus size: 81
29244095 GCTGGAAATT
* * * *
29244105 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCTACATCCGGGCTAAGACCCGAAGGCA
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
*
29244170 TTCGTGCGAGTCATTC
66 TTCGTGCGAGTCATCC
* * * * * *
29244186 -TATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-TGATATCCGGGTTAAGTCCCGTAGGC
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCT-ACATCCGGGCTAAGACCCGAAGGC
* * * *
29244249 CTTGGTGCGGGTTA-CC
65 ATTCGTGCGAGTCATCC
* * *
29244265 ATAACCGGGCTATGTCCCGAAGGCGATTG
1 ATAACCGGGCTAAGACCCGAAGGCAATTG
29244294 ATCGAGTAGC
Statistics
Matches: 86, Mismatches: 20, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
79 2 0.02
80 84 0.98
ACGTcount: A:0.23, C:0.24, G:0.30, T:0.23
Consensus pattern (81 bp):
ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
TTCGTGCGAGTCATCC
Found at i:29252349 original size:40 final size:39
Alignment explanation
Indices: 29252184--29252367 Score: 138
Period size: 40 Copynumber: 4.6 Consensus size: 39
29252174 AAATTGAATG
* * *
29252184 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAAT--T
1 ATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATCGT
* * * * * *
29252224 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-T
* * * * *
29252264 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATC-GT
*
29252304 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
* * *
29252343 GATATCCGGGTTAAGTCCCGTAGGC
1 -ATATCCGGGCTAAGACCCGAAGGC
29252368 CTTGGTGCGG
Statistics
Matches: 113, Mismatches: 26, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
37 4 0.04
38 2 0.02
39 3 0.03
40 104 0.92
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
Found at i:29252392 original size:80 final size:81
Alignment explanation
Indices: 29252224--29252412 Score: 186
Period size: 80 Copynumber: 2.4 Consensus size: 81
29252214 GCTGGAAATT
* * * *
29252224 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCTACATCCGGGCTAAGACCCGAAGGCA
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
*
29252289 TTCGTGCGAGTCATTC
66 TTCGTGCGAGTCATCC
* * * * * *
29252305 -TATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-TGATATCCGGGTTAAGTCCCGTAGGC
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCT-ACATCCGGGCTAAGACCCGAAGGC
* * * *
29252368 CTTGGTGCGGGTTA-CC
65 ATTCGTGCGAGTCATCC
* * *
29252384 ATAACCGGGCTATGTCCCGAAGGCGATTG
1 ATAACCGGGCTAAGACCCGAAGGCAATTG
29252413 ATCGAGTAGC
Statistics
Matches: 86, Mismatches: 20, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
79 2 0.02
80 84 0.98
ACGTcount: A:0.23, C:0.24, G:0.30, T:0.23
Consensus pattern (81 bp):
ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
TTCGTGCGAGTCATCC
Found at i:29264983 original size:14 final size:14
Alignment explanation
Indices: 29264955--29264996 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
29264945 AAATTTGACC
*
29264955 GTTACAATATGATT
1 GTTATAATATGATT
* *
29264969 GTTGTAATTTGATT
1 GTTATAATATGATT
29264983 GTTATAATATGATT
1 GTTATAATATGATT
29264997 ATTAGGATCT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.31, C:0.02, G:0.17, T:0.50
Consensus pattern (14 bp):
GTTATAATATGATT
Found at i:29267388 original size:18 final size:19
Alignment explanation
Indices: 29267365--29267401 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
29267355 AACAAATTAA
29267365 AAAATGAAGAAT-GAAAAT
1 AAAATGAAGAATGGAAAAT
*
29267383 AAAATGAATAATGGAAAAT
1 AAAATGAAGAATGGAAAAT
29267402 TTCTCCCTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.65, C:0.00, G:0.16, T:0.19
Consensus pattern (19 bp):
AAAATGAAGAATGGAAAAT
Found at i:29271244 original size:18 final size:20
Alignment explanation
Indices: 29271221--29271261 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
29271211 TTTGATATTT
29271221 TAATTTT-GTGTAA-TTTTA
1 TAATTTTAGTGTAATTTTTA
*
29271239 TAATTTTAGTTTAATTTTTA
1 TAATTTTAGTGTAATTTTTA
29271259 TAA
1 TAA
29271262 ATAACTAACC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 7 0.35
19 5 0.25
20 8 0.40
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (20 bp):
TAATTTTAGTGTAATTTTTA
Found at i:29278170 original size:29 final size:30
Alignment explanation
Indices: 29278129--29278216 Score: 90
Period size: 31 Copynumber: 2.9 Consensus size: 30
29278119 TAATTTAATG
**
29278129 TGTAATTGCATATATG-AATTTTAATTTGA
1 TGTAATTATATATATGAAATTTTAATTTGA
* *
29278158 TGTAATTATATATGTGAAATTCTAATTGTGA
1 TGTAATTATATATATGAAATTTTAATT-TGA
* *
29278189 T-TCAAATATATATTTGAAATTTTAATTT
1 TGT-AATTATATATATGAAATTTTAATTT
29278217 TGATTTATTC
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
29 13 0.27
30 11 0.22
31 25 0.51
ACGTcount: A:0.36, C:0.03, G:0.11, T:0.49
Consensus pattern (30 bp):
TGTAATTATATATATGAAATTTTAATTTGA
Found at i:29278410 original size:29 final size:30
Alignment explanation
Indices: 29278353--29278411 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
29278343 GAATTGAATC
*
29278353 AAATCAAAATTTCATGTATAAAATCACACA
1 AAATCAAAATTTCATATATAAAATCACACA
* *
29278383 AAATCAAAATTT-ATATATACAATTACACA
1 AAATCAAAATTTCATATATAAAATCACACA
29278412 TTACACCATA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 14 0.54
30 12 0.46
ACGTcount: A:0.54, C:0.15, G:0.02, T:0.29
Consensus pattern (30 bp):
AAATCAAAATTTCATATATAAAATCACACA
Found at i:29280565 original size:34 final size:34
Alignment explanation
Indices: 29280522--29280589 Score: 109
Period size: 34 Copynumber: 2.0 Consensus size: 34
29280512 ATCCATTCAC
* *
29280522 TAAGTCATACAAAACTTTGTCATCTATTTCCTTA
1 TAAGTCATACAAAACATTGTCATCAATTTCCTTA
*
29280556 TAAGTCATACAAAGCATTGTCATCAATTTCCTTA
1 TAAGTCATACAAAACATTGTCATCAATTTCCTTA
29280590 CACACCTATA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.34, C:0.21, G:0.07, T:0.38
Consensus pattern (34 bp):
TAAGTCATACAAAACATTGTCATCAATTTCCTTA
Found at i:29289755 original size:35 final size:35
Alignment explanation
Indices: 29289702--29289794 Score: 109
Period size: 34 Copynumber: 2.7 Consensus size: 35
29289692 ACGACCAGAC
** * * *
29289702 ACACTTGCGAACGTAGTTCACACTTTAG-CAATCTT
1 ACACTTGCGAACACAGTTCACAC-TAAGACAAACAT
*
29289737 ACACTTGCAAACACAGTTCACAC-AAGACAAACAT
1 ACACTTGCGAACACAGTTCACACTAAGACAAACAT
29289771 ACACTTGCGAACACAGTTCACACT
1 ACACTTGCGAACACAGTTCACACT
29289795 GAACATATCT
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
33 2 0.04
34 27 0.55
35 20 0.41
ACGTcount: A:0.37, C:0.29, G:0.12, T:0.23
Consensus pattern (35 bp):
ACACTTGCGAACACAGTTCACACTAAGACAAACAT
Found at i:29301169 original size:47 final size:47
Alignment explanation
Indices: 29300949--29301159 Score: 404
Period size: 47 Copynumber: 4.5 Consensus size: 47
29300939 GTATGAGATA
29300949 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
29300996 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
*
29301043 TATACATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
29301090 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
*
29301137 TATATATGTGATAGGGCCTAATG
1 TATATATGTGATAAGGCCTAATG
29301160 ACTAATGTGA
Statistics
Matches: 161, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 161 1.00
ACGTcount: A:0.32, C:0.09, G:0.29, T:0.30
Consensus pattern (47 bp):
TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
Found at i:29301212 original size:48 final size:48
Alignment explanation
Indices: 29301156--29301362 Score: 333
Period size: 48 Copynumber: 4.3 Consensus size: 48
29301146 GATAGGGCCT
*
29301156 AATGACTAATGTGAAATATATGTGTGATATGTATATGTGGTAAAGCCG
1 AATGGCTAATGTGAAATATATGTGTGATATGTATATGTGGTAAAGCCG
** *
29301204 AATAACTAATATGAAATATATGTGTGATATGTATATGTGGTAAAGCCG
1 AATGGCTAATGTGAAATATATGTGTGATATGTATATGTGGTAAAGCCG
29301252 AATGGCTAATGTGAAATATATGTGTGATATGTATATGTGGTAAAGCCG
1 AATGGCTAATGTGAAATATATGTGTGATATGTATATGTGGTAAAGCCG
* * * * *
29301300 AATGGCGAATGTGAAATATGTATGAGATATGAATATGTGGTAAAGCCG
1 AATGGCTAATGTGAAATATATGTGTGATATGTATATGTGGTAAAGCCG
29301348 AATGGCTAATGTGAA
1 AATGGCTAATGTGAA
29301363 TGTTGTAACA
Statistics
Matches: 148, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 148 1.00
ACGTcount: A:0.37, C:0.06, G:0.26, T:0.31
Consensus pattern (48 bp):
AATGGCTAATGTGAAATATATGTGTGATATGTATATGTGGTAAAGCCG
Found at i:29301515 original size:37 final size:37
Alignment explanation
Indices: 29301407--29301515 Score: 173
Period size: 37 Copynumber: 2.9 Consensus size: 37
29301397 GGAAATATAT
*
29301407 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
*
29301444 TCCGGGTAAGACCCAATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
* * *
29301481 TCCGGGTGAGACCCGATAACTTCGTGTGGAGATTT
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTT
29301516 CGTCTGAGCT
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 66 1.00
ACGTcount: A:0.23, C:0.19, G:0.31, T:0.27
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
Found at i:29311665 original size:11 final size:11
Alignment explanation
Indices: 29311640--29311672 Score: 50
Period size: 10 Copynumber: 3.0 Consensus size: 11
29311630 TTCAAAAAAA
29311640 AAAAGAAAATT
1 AAAAGAAAATT
29311651 -AAAGAAAATT
1 AAAAGAAAATT
29311661 AAAAGATAAATT
1 AAAAGA-AAATT
29311673 GAGTTTTCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 10 0.50
11 5 0.25
12 5 0.25
ACGTcount: A:0.70, C:0.00, G:0.09, T:0.21
Consensus pattern (11 bp):
AAAAGAAAATT
Found at i:29313820 original size:56 final size:55
Alignment explanation
Indices: 29313714--29313823 Score: 157
Period size: 56 Copynumber: 2.0 Consensus size: 55
29313704 TGAGCTTTAC
* *
29313714 GATAAGGGTTTTAGTGTTCTTCTATTTTGCTGACAAAAATTCATGATCTCTATTA
1 GATAAGGGTTTTAGTGTTCTTCTATTTTGCTGAAAAAAATTCAGGATCTCTATTA
* * * *
29313769 GATAAGGGTTTTAGTGATTTTTTTATTTTGCTGAAAAAAATTTAGGCTCTCTATT
1 GATAAGGGTTTTAGTG-TTCTTCTATTTTGCTGAAAAAAATTCAGGATCTCTATT
29313824 CGATTGAAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
55 16 0.33
56 32 0.67
ACGTcount: A:0.27, C:0.10, G:0.17, T:0.45
Consensus pattern (55 bp):
GATAAGGGTTTTAGTGTTCTTCTATTTTGCTGAAAAAAATTCAGGATCTCTATTA
Found at i:29320351 original size:21 final size:22
Alignment explanation
Indices: 29320316--29320357 Score: 68
Period size: 21 Copynumber: 1.9 Consensus size: 22
29320306 TAGTTTTCAA
29320316 ATTGTTTCCATATTGTTTTGTAT
1 ATTGTTT-CATATTGTTTTGTAT
29320339 ATTGTTT-ATATTGTTTTGT
1 ATTGTTTCATATTGTTTTGT
29320358 TATAAATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 12 0.63
23 7 0.37
ACGTcount: A:0.17, C:0.05, G:0.14, T:0.64
Consensus pattern (22 bp):
ATTGTTTCATATTGTTTTGTAT
Found at i:29320367 original size:21 final size:21
Alignment explanation
Indices: 29320325--29320368 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
29320315 AATTGTTTCC
**
29320325 ATATTGTTTTGTATATTGTTT
1 ATATTGTTTTGTATATAATTT
29320346 ATATTGTTTTGT-TATAAATTT
1 ATATTGTTTTGTATAT-AATTT
29320367 AT
1 AT
29320369 TTTCATACTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 3 0.15
21 17 0.85
ACGTcount: A:0.25, C:0.00, G:0.11, T:0.64
Consensus pattern (21 bp):
ATATTGTTTTGTATATAATTT
Found at i:29321428 original size:132 final size:132
Alignment explanation
Indices: 29321191--29321431 Score: 304
Period size: 132 Copynumber: 1.8 Consensus size: 132
29321181 ATTTCCTTTA
* * * ** * *
29321191 AAACGAAGGCGATATTCGATACTTGGTAATTCGTGGAATCGTGCCCTAACGTGTTGGGTTGCAAT
1 AAACGAAGGCCATATGCGATACTTGGGAATTCACGGAATCGTACCCTAACGTGCTGGGTTGCAAT
** ** * *
29321256 TCCTCGTTTGCTCAAAGTAATTGAAGGTCCCTTTAGAATTTCACCCACGGCTATTAAAAAATCCC
66 TCCTCGTTTGCTCAAAACAATCAAAGATCCCTTTAAAATTTCACCCACGGCTATTAAAAAATCCC
29321321 TT
131 TT
*
29321323 AAACGAAGGCCATATGCGATATTTGGGAATTCACGGAATCGTACCCTAACGTGCTGGGTTGCAAT
1 AAACGAAGGCCATATGCGATACTTGGGAATTCACGGAATCGTACCCTAACGTGCTGGGTTGCAAT
* * * *
29321388 TTCTTGTCTT-CTTAAAACAATCAAATATCCCTTTAAAATTTCAC
66 TCCTCGT-TTGCTCAAAACAATCAAAGATCCCTTTAAAATTTCAC
29321432 TCATATATTT
Statistics
Matches: 90, Mismatches: 18, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
132 88 0.98
133 2 0.02
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (132 bp):
AAACGAAGGCCATATGCGATACTTGGGAATTCACGGAATCGTACCCTAACGTGCTGGGTTGCAAT
TCCTCGTTTGCTCAAAACAATCAAAGATCCCTTTAAAATTTCACCCACGGCTATTAAAAAATCCC
TT
Found at i:29321445 original size:132 final size:132
Alignment explanation
Indices: 29321188--29321464 Score: 297
Period size: 132 Copynumber: 2.1 Consensus size: 132
29321178 ACAATTTCCT
* * * ** * *
29321188 TTAAAACGAAGGCGATATTCGATACTTGGTAATTCGTGGAATCGTGCCCTAACGTGTTGGGTTGC
1 TTAAAACGAAGGCCATATGCGATACTTGGGAATTCACGGAATCGTACCCTAACGTGCTGGGTTGC
** ** * * * *
29321253 AATTCCTCGTTTGCTCAAAGTAATTGAAGGTCCCTTTAGAATTTCACCCACGGCTATTAAAAAAT
66 AATTCCTCGTTTGCTCAAAACAATCAAAGATCCCTTTAAAATTTCACCCACAGATATT-AAAAAT
29321318 CCC
130 CCC
*
29321321 TT-AAACGAAGGCCATATGCGATATTTGGGAATTCACGGAATCGTACCCTAACGTGCTGGGTTGC
1 TTAAAACGAAGGCCATATGCGATACTTGGGAATTCACGGAATCGTACCCTAACGTGCTGGGTTGC
* * * * * * * *
29321385 AATTTCTTGTCTT-CTTAAAACAATCAAATATCCCTTTAAAATTTCACTCATATATTTTAAAAAT
66 AATTCCTCGT-TTGCTCAAAACAATCAAAGATCCCTTTAAAATTTCACCCACAGATATTAAAAAT
*
29321449 CCT
130 CCC
29321452 TTAAAACGAAGGC
1 TTAAAACGAAGGC
29321465 AATACTCGGG
Statistics
Matches: 117, Mismatches: 25, Indels: 5
0.80 0.17 0.03
Matches are distributed among these distances:
131 10 0.09
132 103 0.88
133 4 0.03
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Consensus pattern (132 bp):
TTAAAACGAAGGCCATATGCGATACTTGGGAATTCACGGAATCGTACCCTAACGTGCTGGGTTGC
AATTCCTCGTTTGCTCAAAACAATCAAAGATCCCTTTAAAATTTCACCCACAGATATTAAAAATC
CC
Found at i:29321536 original size:131 final size:131
Alignment explanation
Indices: 29321366--29321696 Score: 344
Period size: 132 Copynumber: 2.5 Consensus size: 131
29321356 CGGAATCGTA
* * * * * *
29321366 CCCTAACGTGCTGGGTTGCAATTTCTTGTCTTCTT-AAAACAATCAAATATCCCTTTAAAATTTC
1 CCCTATCGTGCTGGGTTGCGATTTCTCGT-TTGTTCAAAACAATCGAATATCCCTTTAGAATTTC
* *
29321430 ACTCATATATT-TTAAAAATCCTTT-AAAACGAAGGCAATACTCGGGGTTTGACAATTCGAGAAT
65 ACTCATAT-TTATTAAAAA-CCTTTCAAAACGAAGGCAATACTAGAGGTTTGACAATTCGAGAAT
29321493 CATG
128 CATG
* * * ** *
29321497 CCCTATCGTGTTGGGTTGTGATTTCTCGTTTGTTCAAAACAATCGAATATTCCTTTAGGTTTTTT
1 CCCTATCGTGCTGGGTTGCGATTTCTCGTTTGTTCAAAACAATCGAATATCCCTTTA-GAATTTC
* * ** * * * **
29321562 ACTCATGTTTATTAAAAACCTTTCAAAACGAAGGCGATTTTAGATGTTTGGCAATTTGAGAATTG
65 ACTCATATTTATTAAAAACCTTTCAAAACGAAGGCAATACTAGAGGTTTGACAATTCGAGAATCA
29321627 TG
130 TG
* * * * * *
29321629 CCCTATCGTGCTGGGTTGCGCTTTTTCATTTGTTCAAGACAATCGAAGATCCCTTTGGAATTTCA
1 CCCTATCGTGCTGGGTTGCGATTTCTCGTTTGTTCAAAACAATCGAATATCCCTTTAGAATTTCA
29321694 CTC
66 CTC
29321697 TTCTTTTTTA
Statistics
Matches: 161, Mismatches: 35, Indels: 8
0.79 0.17 0.04
Matches are distributed among these distances:
130 4 0.02
131 59 0.37
132 98 0.61
ACGTcount: A:0.27, C:0.19, G:0.17, T:0.37
Consensus pattern (131 bp):
CCCTATCGTGCTGGGTTGCGATTTCTCGTTTGTTCAAAACAATCGAATATCCCTTTAGAATTTCA
CTCATATTTATTAAAAACCTTTCAAAACGAAGGCAATACTAGAGGTTTGACAATTCGAGAATCAT
G
Found at i:29338322 original size:15 final size:17
Alignment explanation
Indices: 29338304--29338335 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
29338294 TAGCATAATT
29338304 TACCAAA-TCA-ATTCA
1 TACCAAACTCACATTCA
29338319 TACCAAACTCACATTCA
1 TACCAAACTCACATTCA
29338336 CAAGTATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 3 0.20
17 5 0.33
ACGTcount: A:0.44, C:0.31, G:0.00, T:0.25
Consensus pattern (17 bp):
TACCAAACTCACATTCA
Found at i:29340890 original size:147 final size:147
Alignment explanation
Indices: 29340623--29340918 Score: 556
Period size: 147 Copynumber: 2.0 Consensus size: 147
29340613 CATCTAAGGG
*
29340623 TCTGAGCCATTGGAAGATGATCAAGGTAAGGAAAGTATGGTTTTGATGGAAGCCAATCCGAGAGA
1 TCTGAGCCATTGGAAGATGATCAAGGTAAGAAAAGTATGGTTTTGATGGAAGCCAATCCGAGAGA
*
29340688 CTATGTTCAACTAGCACAATTTGAACAATTGGAGTTAGAAGCTTGAGAATACGCACAACAAAAGT
66 CTATGTTCAACTAGCACAATTTGAACAATTGGAGTTAGAAGATTGAGAATACGCACAACAAAAGT
*
29340753 TGTCAATCGATGAACCA
131 TGTCAATCGAGGAACCA
29340770 TCTGAGCCATTGGAAGATGATCAAGGTAAGAAAAGTATGGTTTTGATGGAAGCCAATCCGAGAGA
1 TCTGAGCCATTGGAAGATGATCAAGGTAAGAAAAGTATGGTTTTGATGGAAGCCAATCCGAGAGA
*
29340835 CTATGTTCAACTAGCACAATTTGAACAATTGGAGTTAGAAGATTGAGAATACGCACAACCAAAGT
66 CTATGTTCAACTAGCACAATTTGAACAATTGGAGTTAGAAGATTGAGAATACGCACAACAAAAGT
29340900 TGTCAATCGAGGAACCA
131 TGTCAATCGAGGAACCA
29340917 TC
1 TC
29340919 CAAACTTGAA
Statistics
Matches: 145, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
147 145 1.00
ACGTcount: A:0.37, C:0.16, G:0.24, T:0.24
Consensus pattern (147 bp):
TCTGAGCCATTGGAAGATGATCAAGGTAAGAAAAGTATGGTTTTGATGGAAGCCAATCCGAGAGA
CTATGTTCAACTAGCACAATTTGAACAATTGGAGTTAGAAGATTGAGAATACGCACAACAAAAGT
TGTCAATCGAGGAACCA
Found at i:29342453 original size:28 final size:28
Alignment explanation
Indices: 29342419--29342479 Score: 115
Period size: 28 Copynumber: 2.2 Consensus size: 28
29342409 ATTGCTTACG
29342419 AAGAATGCATGATGAAATTTAATGTAGC
1 AAGAATGCATGATGAAATTTAATGTAGC
29342447 AAGAATGCATGATGAAATTTAATGTAGC
1 AAGAATGCATGATGAAATTTAATGTAGC
29342475 -AGAAT
1 AAGAAT
29342480 AATGATTGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 5 0.15
28 28 0.85
ACGTcount: A:0.44, C:0.07, G:0.21, T:0.28
Consensus pattern (28 bp):
AAGAATGCATGATGAAATTTAATGTAGC
Found at i:29342601 original size:48 final size:48
Alignment explanation
Indices: 29342545--29342907 Score: 335
Period size: 48 Copynumber: 7.6 Consensus size: 48
29342535 GTGTGCTAGC
29342545 GTAAGACCATGTCTGGGACATGGCATCGGCCATGATATGAGAGCCAGT
1 GTAAGACCATGTCTGGGACATGGCATCGGCCATGATATGAGAGCCAGT
* * * *
29342593 GTAAGACCATGTTTGGAACATGGCATCGGCAATG-TAATGAGAGGCAGT
1 GTAAGACCATGTCTGGGACATGGCATCGGCCATGAT-ATGAGAGCCAGT
* * * * *
29342641 GTAAGACTATGTCTGGGACATTG-ATC-GACATTGATATGTGCA-CTAGT
1 GTAAGACCATGTCTGGGACATGGCATCGGCCA-TGATATGAG-AGCCAGT
* *
29342688 GTAAAACCATGTCTGGGACATGGCATCGGCCACGATATGAGAGCCAGT
1 GTAAGACCATGTCTGGGACATGGCATCGGCCATGATATGAGAGCCAGT
* * * * *
29342736 GTAAGACCATGTTTGGAACATGGCATCAGACATG-TAATGAGAGCCAAT
1 GTAAGACCATGTCTGGGACATGGCATCGGCCATGAT-ATGAGAGCCAGT
** ** * * *
29342784 GTAAGATAATGTCTAAGACATGGCATCGG-TATTGATATGTGCA-CTAGT
1 GTAAGACCATGTCTGGGACATGGCATCGGCCA-TGATATGAG-AGCCAGT
* * * * * *
29342832 GTAAAACCATGTCTGGGATATGGAATTGGCCAGGATATGAGAGCTAGT
1 GTAAGACCATGTCTGGGACATGGCATCGGCCATGATATGAGAGCCAGT
* * *
29342880 GTAAGACTATGTTTGGAACATGGCATCG
1 GTAAGACCATGTCTGGGACATGGCATCG
29342908 ACAATTCACC
Statistics
Matches: 246, Mismatches: 56, Indels: 26
0.75 0.17 0.08
Matches are distributed among these distances:
46 2 0.01
47 37 0.15
48 201 0.82
49 6 0.02
ACGTcount: A:0.30, C:0.16, G:0.28, T:0.25
Consensus pattern (48 bp):
GTAAGACCATGTCTGGGACATGGCATCGGCCATGATATGAGAGCCAGT
Found at i:29342788 original size:143 final size:143
Alignment explanation
Indices: 29342530--29342910 Score: 550
Period size: 143 Copynumber: 2.7 Consensus size: 143
29342520 ACATTTGGGC
** * * *
29342530 GATATGTGTGCTAGCGTAAGACCATGTCTGGGACATGGCATCGGCCATGATATGAGAGCCAGTGT
1 GATATGTGCACTAGTGTAAAACCATGTCTGGGACATGGCATCGGCCACGATATGAGAGCCAGTGT
* * * **
29342595 AAGACCATGTTTGGAACATGGCATCGGCAATGTAATGAGAGGCAGTGTAAGACT-ATGTCTGGGA
66 AAGACCATGTTTGGAACATGGCATCGAC-ATGTAATGAGAGCCAATGTAAGA-TAATGTCTAAGA
*
29342659 CATTG-ATCGACATT
129 CATGGCATCGACATT
29342673 GATATGTGCACTAGTGTAAAACCATGTCTGGGACATGGCATCGGCCACGATATGAGAGCCAGTGT
1 GATATGTGCACTAGTGTAAAACCATGTCTGGGACATGGCATCGGCCACGATATGAGAGCCAGTGT
29342738 AAGACCATGTTTGGAACATGGCATCAGACATGTAATGAGAGCCAATGTAAGATAATGTCTAAGAC
66 AAGACCATGTTTGGAACATGGCATC-GACATGTAATGAGAGCCAATGTAAGATAATGTCTAAGAC
**
29342803 ATGGCATCGGTATT
130 ATGGCATCGACATT
* * * * *
29342817 GATATGTGCACTAGTGTAAAACCATGTCTGGGATATGGAATTGGCCAGGATATGAGAGCTAGTGT
1 GATATGTGCACTAGTGTAAAACCATGTCTGGGACATGGCATCGGCCACGATATGAGAGCCAGTGT
*
29342882 AAGACTATGTTTGGAACATGGCATCGACA
66 AAGACCATGTTTGGAACATGGCATCGACA
29342911 ATTCACCCTC
Statistics
Matches: 216, Mismatches: 19, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
142 1 0.00
143 122 0.56
144 93 0.43
ACGTcount: A:0.30, C:0.16, G:0.28, T:0.25
Consensus pattern (143 bp):
GATATGTGCACTAGTGTAAAACCATGTCTGGGACATGGCATCGGCCACGATATGAGAGCCAGTGT
AAGACCATGTTTGGAACATGGCATCGACATGTAATGAGAGCCAATGTAAGATAATGTCTAAGACA
TGGCATCGACATT
Found at i:29343819 original size:16 final size:17
Alignment explanation
Indices: 29343792--29343823 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
29343782 AAGTTTAGGG
29343792 CAAAACTATAATTTTGC
1 CAAAACTATAATTTTGC
29343809 CAAAA-TATAATTTTG
1 CAAAACTATAATTTTG
29343824 GGTCAATTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.44, C:0.12, G:0.06, T:0.38
Consensus pattern (17 bp):
CAAAACTATAATTTTGC
Found at i:29347259 original size:15 final size:15
Alignment explanation
Indices: 29347239--29347307 Score: 84
Period size: 15 Copynumber: 4.6 Consensus size: 15
29347229 GTATCTTGGG
29347239 TTTCTTTATCCTGGA
1 TTTCTTTATCCTGGA
* *
29347254 TCTCTTTATTCTGGA
1 TTTCTTTATCCTGGA
* *
29347269 TTTCTTTATTCTGGG
1 TTTCTTTATCCTGGA
* *
29347284 TTTCTCTATCTTGGA
1 TTTCTTTATCCTGGA
29347299 TTTCTTTAT
1 TTTCTTTAT
29347308 TCGGTTTTCT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 45 1.00
ACGTcount: A:0.12, C:0.17, G:0.13, T:0.58
Consensus pattern (15 bp):
TTTCTTTATCCTGGA
Found at i:29347308 original size:30 final size:30
Alignment explanation
Indices: 29347230--29347317 Score: 99
Period size: 30 Copynumber: 3.0 Consensus size: 30
29347220 TATTCTATCG
* * * *
29347230 TATCTTGGGTTTCTTTATCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTCTGGATTTCTC
*
29347260 TAT-TCTGGATTTCTTTATTCTGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCTGGATTTCTC
*
29347290 TATCTTGGATTTCTTTATTC-GGTTTTCT
1 TATCTTGGATTTCTTTATTCTGGATTTCT
29347318 TGTTATCTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
29 8 0.16
30 41 0.82
31 1 0.02
ACGTcount: A:0.10, C:0.17, G:0.16, T:0.57
Consensus pattern (30 bp):
TATCTTGGATTTCTTTATTCTGGATTTCTC
Found at i:29348823 original size:227 final size:227
Alignment explanation
Indices: 29348416--29348874 Score: 846
Period size: 227 Copynumber: 2.0 Consensus size: 227
29348406 GGAGAGTTGT
*
29348416 AATATCCTAATTTTGGGCCTAGTCGGAATAGTGGTTTCGTGACCACAAAATCCGAGATAGAAATA
1 AATATCCTAATTTTGGGCCTAGTCGGAATAGTGGTTTCGTGACCACAAAATCCAAGATAGAAATA
*
29348481 ATTATTTTATGATTATTTTAAGGTCTATGATATGATTTCATGATTGTGTGAAAATTTCGTGAAGA
66 ATTATTTTATGATTATTTTAAGGTCTATGATATGATTGCATGATTGTGTGAAAATTTCGTGAAGA
*
29348546 AATTTTATGCATAAAGTGCTTAAATTGAAATTAGGGACTAAATCGAATAATTTGTAAAACTTGCA
131 AATTTTATGCATAAAGTGCTTAAATTGAAATTAGGGACTAAATCGAATAATTTGCAAAACTTGCA
29348611 TTCTAGAAGTTTCTAGTATGAAATTGTTTTGA
196 TTCTAGAAGTTTCTAGTATGAAATTGTTTTGA
* * * *
29348643 AATATCTTGATTTTGGGCCTGGTCGGAATAGTGGTTTCGTGACCATAAAATCCAAGATAGAAATA
1 AATATCCTAATTTTGGGCCTAGTCGGAATAGTGGTTTCGTGACCACAAAATCCAAGATAGAAATA
29348708 ATTATTTTATGATTATTTTAAGGTCTATGATATGATTGCATGATTGTGTGAAAATTTCGTGAAGA
66 ATTATTTTATGATTATTTTAAGGTCTATGATATGATTGCATGATTGTGTGAAAATTTCGTGAAGA
*
29348773 AATTTTATGCATAAAGTGCTTAAATTGAAATTAGGGACTAAATTGAATAATTTGCAAAACTTGCA
131 AATTTTATGCATAAAGTGCTTAAATTGAAATTAGGGACTAAATCGAATAATTTGCAAAACTTGCA
29348838 TTCTAGAAGTTTCTAGTATGAAATTGTTTTGA
196 TTCTAGAAGTTTCTAGTATGAAATTGTTTTGA
29348870 AATAT
1 AATAT
29348875 TAATTAGGAG
Statistics
Matches: 224, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
227 224 1.00
ACGTcount: A:0.34, C:0.09, G:0.19, T:0.38
Consensus pattern (227 bp):
AATATCCTAATTTTGGGCCTAGTCGGAATAGTGGTTTCGTGACCACAAAATCCAAGATAGAAATA
ATTATTTTATGATTATTTTAAGGTCTATGATATGATTGCATGATTGTGTGAAAATTTCGTGAAGA
AATTTTATGCATAAAGTGCTTAAATTGAAATTAGGGACTAAATCGAATAATTTGCAAAACTTGCA
TTCTAGAAGTTTCTAGTATGAAATTGTTTTGA
Found at i:29349512 original size:16 final size:17
Alignment explanation
Indices: 29349485--29349516 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
29349475 AAGTTTAGGG
29349485 CAAAACTATAATTTTGC
1 CAAAACTATAATTTTGC
29349502 CAAAA-TATAATTTTG
1 CAAAACTATAATTTTG
29349517 GGTCAATTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.44, C:0.12, G:0.06, T:0.38
Consensus pattern (17 bp):
CAAAACTATAATTTTGC
Found at i:29349978 original size:46 final size:46
Alignment explanation
Indices: 29349928--29350056 Score: 215
Period size: 46 Copynumber: 2.8 Consensus size: 46
29349918 TGGTTGAGCA
29349928 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
29349974 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
29350020 CCCGAGCTCATTGAGTTGATGT-CGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGA-GTCCGAGTTCACTTATGG
29350057 GCGGGTTACA
Statistics
Matches: 79, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
46 77 0.97
47 2 0.03
ACGTcount: A:0.21, C:0.20, G:0.28, T:0.31
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:29352671 original size:10 final size:10
Alignment explanation
Indices: 29352656--29352686 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
29352646 CGATTCTTTT
*
29352656 TATTTTATTA
1 TATTTTGTTA
29352666 TATTTTGTTA
1 TATTTTGTTA
29352676 TATTTTGTTA
1 TATTTTGTTA
29352686 T
1 T
29352687 CATATGAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.23, C:0.00, G:0.06, T:0.71
Consensus pattern (10 bp):
TATTTTGTTA
Found at i:29352965 original size:51 final size:50
Alignment explanation
Indices: 29352837--29352975 Score: 165
Period size: 49 Copynumber: 2.8 Consensus size: 50
29352827 TATTGTGATG
*** * * * *
29352837 TCACGTGTGTAGTACTAAGTGCAGGCTACTACATGTACCGGATAATTGGT
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGACAATTCGA
29352887 TGCA--TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGACAACTTCGA
1 T-CACGTGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGACAA-TTCGA
* *
29352937 TCACGTGTGTAGTACTTAGTGCAGGCTACTATGCATACC
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTATGCGTACC
29352976 AGATAGCCTT
Statistics
Matches: 76, Mismatches: 9, Indels: 7
0.83 0.10 0.08
Matches are distributed among these distances:
49 37 0.49
50 5 0.07
51 34 0.45
ACGTcount: A:0.25, C:0.22, G:0.24, T:0.29
Consensus pattern (50 bp):
TCACGTGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGACAATTCGA
Found at i:29357468 original size:9 final size:9
Alignment explanation
Indices: 29357454--29357480 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
29357444 TGACTTCGAC
29357454 GGAGTTAAA
1 GGAGTTAAA
29357463 GGAGTTAAA
1 GGAGTTAAA
29357472 GGAGTTAAA
1 GGAGTTAAA
29357481 AGCACAGTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.33, T:0.22
Consensus pattern (9 bp):
GGAGTTAAA
Found at i:29359190 original size:26 final size:26
Alignment explanation
Indices: 29359155--29359207 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
29359145 TGGAAGAAAG
*
29359155 TCCTTCGATTTGGTAGGAAAGAAAAA
1 TCCTTAGATTTGGTAGGAAAGAAAAA
29359181 TCCTTAGATTTGGTAGGAAAGAAAAA
1 TCCTTAGATTTGGTAGGAAAGAAAAA
29359207 T
1 T
29359208 TAAGTTCAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.40, C:0.09, G:0.23, T:0.28
Consensus pattern (26 bp):
TCCTTAGATTTGGTAGGAAAGAAAAA
Found at i:29360865 original size:48 final size:47
Alignment explanation
Indices: 29360808--29361121 Score: 337
Period size: 48 Copynumber: 6.6 Consensus size: 47
29360798 GTGTGCTAGC
* *
29360808 GTAAGACCATGTCTGGGACATGGCATCTGCCACGATATGAGAGCCAGT
1 GTAAGACCATGTCTGGAACATGGCATC-GCCATGATATGAGAGCCAGT
* * * * *
29360856 GTAAGACCATGTTTGGAACATGACATCGGCAATG-TAATCAGAGTCAGT
1 GTAAGACCATGTCTGGAACATGGCATC-GCCATGAT-ATGAGAGCCAGT
* ** * * *
29360904 GTAAGACCATGTCTGGAACATTGCATCGGTATTGATATGTGCGCTAGT
1 GTAAGACCATGTCTGGAACATGGCATCGCCA-TGATATGAGAGCCAGT
*
29360952 GTAAGACCATGTCTGGGACATGGCATCGGCCATGATATGAGAGCCAGT
1 GTAAGACCATGTCTGGAACATGGCATC-GCCATGATATGAGAGCCAGT
* * *
29361000 GTAAGACCATGTTTGGAACATGGCATCGACAAT-ATAATGAGAGACAGT
1 GTAAGACCATGTCTGGAACATGGCATCG-CCATGAT-ATGAGAGCCAGT
* * * *
29361048 GTAAGACCATGTCTGGGACATGGTATCGACCTTGATATGAGAGCTAGT
1 GTAAGACCATGTCTGGAACATGGCATCG-CCATGATATGAGAGCCAGT
29361096 GTAAGACCATGGT-TGGAACATGGCAT
1 GTAAGACCAT-GTCTGGAACATGGCAT
29361122 TGGCAATTCA
Statistics
Matches: 220, Mismatches: 38, Indels: 16
0.80 0.14 0.06
Matches are distributed among these distances:
47 6 0.03
48 207 0.94
49 7 0.03
ACGTcount: A:0.30, C:0.18, G:0.28, T:0.25
Consensus pattern (47 bp):
GTAAGACCATGTCTGGAACATGGCATCGCCATGATATGAGAGCCAGT
Found at i:29361054 original size:144 final size:144
Alignment explanation
Indices: 29360794--29361121 Score: 478
Period size: 144 Copynumber: 2.3 Consensus size: 144
29360784 CATTTGGGTA
* * *
29360794 ATATGTGTGCTAGCGTAAGACCATGTCTGGGACATGGCATCTGCCACGATATGAGAGCCAGTGTA
1 ATATGTGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCACGATATGAGAGCCAGTGTA
* * *
29360859 AGACCATGTTTGGAACATGACATCGGCAATGTAATCAGAGTCAGTGTAAGACCATGTCTGGAACA
66 AGACCATGTTTGGAACATGACATCGACAATATAATCAGAGACAGTGTAAGACCATGTCTGGAACA
* **
29360924 TTGCATCGGTATTG
131 TGGCATCGACATTG
* *
29360938 ATATGTGCGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCATGATATGAGAGCCAGTGTA
1 ATATGTGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCACGATATGAGAGCCAGTGTA
* * *
29361003 AGACCATGTTTGGAACATGGCATCGACAATATAATGAGAGACAGTGTAAGACCATGTCTGGGACA
66 AGACCATGTTTGGAACATGACATCGACAATATAATCAGAGACAGTGTAAGACCATGTCTGGAACA
* *
29361068 TGGTATCGACCTTG
131 TGGCATCGACATTG
* *
29361082 ATATGAGAGCTAGTGTAAGACCATGGT-TGGAACATGGCAT
1 ATATGTGAGCTAGTGTAAGACCAT-GTCTGGGACATGGCAT
29361122 TGGCAATTCA
Statistics
Matches: 165, Mismatches: 18, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
144 163 0.99
145 2 0.01
ACGTcount: A:0.29, C:0.18, G:0.28, T:0.25
Consensus pattern (144 bp):
ATATGTGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCACGATATGAGAGCCAGTGTA
AGACCATGTTTGGAACATGACATCGACAATATAATCAGAGACAGTGTAAGACCATGTCTGGAACA
TGGCATCGACATTG
Found at i:29368478 original size:3 final size:3
Alignment explanation
Indices: 29368455--29368508 Score: 58
Period size: 3 Copynumber: 18.3 Consensus size: 3
29368445 ATTCCTTTAC
* * *
29368455 ATT ATT -TT AATT ATT -TT ATT ATT ACT ATT ATT ATT CTT ATT ATC
1 ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
29368499 ATT ATT ATT A
1 ATT ATT ATT A
29368509 ATCTTATTTC
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
2 4 0.10
3 36 0.86
4 2 0.05
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:29376017 original size:49 final size:48
Alignment explanation
Indices: 29375901--29376166 Score: 250
Period size: 47 Copynumber: 5.6 Consensus size: 48
29375891 GGTAGAATGC
* * * *
29375901 CGATGTCATGTCTCAGACATGGTCTTACACTGGCTCAT-ATCTC-AAGT
1 CGATGCCATGTCCCAGACATGGTCTTACACTGACT-ATCATCTCGAGGT
* *
29375948 CGATGCCATATCCCAAACATGGTCTTACACTGACTATCATCATCGAGGT
1 CGATGCCATGTCCCAGACATGGTCTTACACTGACTATCATC-TCGAGGT
* * * *
29375997 CGACGCCATGTCCCAGACATGGTCTTACACT-AGCTCTCACATACTCG-TGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTGA-CTAT--CAT-CTCGAGGT
*
29376047 CGATGCCATGTCCCAGACATGGTCTTACACTGAC-AT-ATCTCGTAGCT
1 CGATGCCATGTCCCAGACATGGTCTTACACTGACTATCATCTCG-AGGT
* *
29376094 -GATG-CATGTCCCAGACAT-GTCTTACACT-AGCT-TACGTCTCGAGGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTGA-CTAT-CATCTCGAGGT
29376139 CGATG-CATGTCCCAGACATGGTCTTACA
1 CGATGCCATGTCCCAGACATGGTCTTACA
29376167 TTGGCTCATA
Statistics
Matches: 183, Mismatches: 20, Indels: 32
0.78 0.09 0.14
Matches are distributed among these distances:
43 1 0.01
44 12 0.07
45 20 0.11
46 31 0.17
47 41 0.22
48 3 0.02
49 35 0.19
50 32 0.17
51 7 0.04
52 1 0.01
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.27
Consensus pattern (48 bp):
CGATGCCATGTCCCAGACATGGTCTTACACTGACTATCATCTCGAGGT
Found at i:29376075 original size:99 final size:94
Alignment explanation
Indices: 29375907--29376166 Score: 309
Period size: 99 Copynumber: 2.8 Consensus size: 94
29375897 ATGCCGATGT
* * * * * * *
29375907 CATGTCTCAGACATGGTCTTACACT-G-GCTCATATCTCAAGTCGATGCCATATCCCAAACATGG
1 CATGTCCCAGACATGGTCTTACACTAGCTCTCACATCTCGAGCCGATGCCATGTCCCAGACATGG
*
29375970 TCTTACACTGACTATCATCATCG-AGGTCGACG
66 TCTTACACTGAC-AT-ATC-TCGTAGCT-GACG
*
29376002 CCATGTCCCAGACATGGTCTTACACTAGCTCTCACATACTCGTGCCGATGCCATGTCCCAGACAT
1 -CATGTCCCAGACATGGTCTTACACTAGCTCTCACAT-CTCGAGCCGATGCCATGTCCCAGACAT
*
29376067 GGTCTTACACTGACATATCTCGTAGCTGATG
64 GGTCTTACACTGACATATCTCGTAGCTGACG
*
29376098 CATGTCCCAGACAT-GTCTTACACTAGCT-T-ACGTCTCGAGGCCGATG-CATGTCCCAGACATG
1 CATGTCCCAGACATGGTCTTACACTAGCTCTCACATCTCGA-GCCGATGCCATGTCCCAGACATG
29376159 GTCTTACA
65 GTCTTACA
29376167 TTGGCTCATA
Statistics
Matches: 147, Mismatches: 12, Indels: 15
0.84 0.07 0.09
Matches are distributed among these distances:
91 27 0.18
92 10 0.07
93 1 0.01
94 14 0.10
95 14 0.10
96 30 0.20
97 7 0.05
98 8 0.05
99 36 0.24
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.27
Consensus pattern (94 bp):
CATGTCCCAGACATGGTCTTACACTAGCTCTCACATCTCGAGCCGATGCCATGTCCCAGACATGG
TCTTACACTGACATATCTCGTAGCTGACG
Found at i:29385938 original size:27 final size:26
Alignment explanation
Indices: 29385894--29385945 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
29385884 CTCGTTGCAA
*
29385894 TCTGGTGGCCTCGCCACATATATCTGT
1 TCTGGTGACCTCGCCACA-ATATCTGT
* *
29385921 TCTGGTGACTTCGTCACAATATCTG
1 TCTGGTGACCTCGCCACAATATCTG
29385946 GCAGCCTCGT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.17, C:0.27, G:0.21, T:0.35
Consensus pattern (26 bp):
TCTGGTGACCTCGCCACAATATCTGT
Found at i:29396646 original size:16 final size:16
Alignment explanation
Indices: 29396625--29396656 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
29396615 ATGGGCCGAA
29396625 AATGGGCCAACGGGCC
1 AATGGGCCAACGGGCC
29396641 AATGGGCCAACGGGCC
1 AATGGGCCAACGGGCC
29396657 CACTTTGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.31, G:0.38, T:0.06
Consensus pattern (16 bp):
AATGGGCCAACGGGCC
Found at i:29396951 original size:27 final size:26
Alignment explanation
Indices: 29396907--29396958 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
29396897 CTCGCTGCAA
*
29396907 TCTGGTGGCCTCGCCACATATATCTGT
1 TCTGGTGACCTCGCCACA-ATATCTGT
* *
29396934 TCTGGTGACTTCGTCACAATATCTG
1 TCTGGTGACCTCGCCACAATATCTG
29396959 GTAGCCTCGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.17, C:0.27, G:0.21, T:0.35
Consensus pattern (26 bp):
TCTGGTGACCTCGCCACAATATCTGT
Found at i:29396998 original size:2 final size:2
Alignment explanation
Indices: 29396991--29397016 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
29396981 GCTTTGCCAC
29396991 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
29397017 CTGTTCTGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29407841 original size:67 final size:68
Alignment explanation
Indices: 29407770--29407957 Score: 170
Period size: 67 Copynumber: 2.8 Consensus size: 68
29407760 AAGTTCCATA
* ** *
29407770 TTTATTGTCT-TAGTGGACTTAATTTTTTGCCATAGTC-GAGCTATGGTCTTACACAATATACCT
1 TTTATTGTCTCTAGTGGACTTAATATGCTACCATAG-CAGAGCTATGGTCTTACACAATATACCT
*
29407833 CGTG
65 CATG
* ** * *
29407837 TTTATTGTCTCAACAGG-CTTTATATGCTACTATAGCAGAGCTATGGTCTTACACAATATACCTC
1 TTTATTGTCTCTAGTGGACTTAATATGCTACCATAGCAGAGCTATGGTCTTACACAATATACCTC
29407901 ATG
66 ATG
* ** * * * *
29407904 TTTACTGTCTCT-GTGGACTCCATATGTTGCCATAACCA-AGCTATGGTATTACAC
1 TTTATTGTCTCTAGTGGACTTAATATGCTACCAT-AGCAGAGCTATGGTCTTACAC
29407958 TCTAAACCTG
Statistics
Matches: 96, Mismatches: 21, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
66 3 0.03
67 87 0.91
68 6 0.06
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.38
Consensus pattern (68 bp):
TTTATTGTCTCTAGTGGACTTAATATGCTACCATAGCAGAGCTATGGTCTTACACAATATACCTC
ATG
Found at i:29409979 original size:46 final size:44
Alignment explanation
Indices: 29409912--29410085 Score: 188
Period size: 46 Copynumber: 3.8 Consensus size: 44
29409902 TGTAACCCGC
29409912 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCTTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGC-TTCG-AT
* * *
29409958 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--GCTTCGAT
* *** * *
29410004 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGTAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGGGC-TTCG-AT
*
29410051 CCATAAGTGAACT-GGACTCAACTCAACGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG
29410086 ATGCTCAACC
Statistics
Matches: 107, Mismatches: 16, Indels: 11
0.80 0.12 0.08
Matches are distributed among these distances:
45 23 0.21
46 48 0.45
47 34 0.32
48 2 0.02
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (44 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCTTCGAT
Found at i:29410033 original size:93 final size:92
Alignment explanation
Indices: 29409920--29410089 Score: 286
Period size: 93 Copynumber: 1.8 Consensus size: 92
29409910 GCCCATAAGT
* *
29409920 GAACTCGGACTCAACTCAACGAGCTCGGGCTTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACT-GGACTCAACTCAA
29409985 CGAGCTCGGATGCCTAGTTACATCTCTC
65 CGAGCTCGGATGCCTAGTTACATCTCTC
* *
29410013 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGTATCCATAAGTGAACTGGACTCAACTCAAC
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTGGACTCAACTCAAC
*
29410078 GAGTTCGGATGC
66 GAGCTCGGATGC
29410090 TCAACCATCC
Statistics
Matches: 72, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
92 25 0.35
93 47 0.65
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (92 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTGGACTCAACTCAAC
GAGCTCGGATGCCTAGTTACATCTCTC
Found at i:29417505 original size:3 final size:3
Alignment explanation
Indices: 29417497--29417535 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
29417487 TTTAATTCTT
* * *
29417497 TTA TTA TTA CTA TTA TTA TTC TTA TTA TCA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
29417536 ATCTTATTTA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.31, C:0.08, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:29419623 original size:29 final size:29
Alignment explanation
Indices: 29419591--29419652 Score: 115
Period size: 29 Copynumber: 2.1 Consensus size: 29
29419581 ATTGAGGACA
*
29419591 ATGTACATCTTAAGTGTGGGGAGGTTCTG
1 ATGTACATCTTAAGTGTGGGGAGGTTATG
29419620 ATGTACATCTTAAGTGTGGGGAGGTTATG
1 ATGTACATCTTAAGTGTGGGGAGGTTATG
29419649 ATGT
1 ATGT
29419653 TATGATAATC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.23, C:0.08, G:0.34, T:0.35
Consensus pattern (29 bp):
ATGTACATCTTAAGTGTGGGGAGGTTATG
Found at i:29425243 original size:28 final size:28
Alignment explanation
Indices: 29425197--29425265 Score: 122
Period size: 28 Copynumber: 2.5 Consensus size: 28
29425187 TTTAAAACCC
*
29425197 TAGGGGT-ATATCGGTAATTTTGCTCTT
1 TAGGGGTAATTTCGGTAATTTTGCTCTT
29425224 TAGGGGTAATTTCGGTAATTTTGCTCTT
1 TAGGGGTAATTTCGGTAATTTTGCTCTT
29425252 TAGGGGTAATTTCG
1 TAGGGGTAATTTCG
29425266 TGATCTACGC
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 7 0.17
28 33 0.82
ACGTcount: A:0.19, C:0.10, G:0.28, T:0.43
Consensus pattern (28 bp):
TAGGGGTAATTTCGGTAATTTTGCTCTT
Found at i:29426916 original size:20 final size:20
Alignment explanation
Indices: 29426893--29426930 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
29426883 CACATCCAAA
*
29426893 TACAAAATTTTAAAAATCTT
1 TACAAAATATTAAAAATCTT
*
29426913 TACAAAATATTGAAAATC
1 TACAAAATATTAAAAATC
29426931 GCGAATAAAC
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:0.53, C:0.11, G:0.03, T:0.34
Consensus pattern (20 bp):
TACAAAATATTAAAAATCTT
Found at i:29429623 original size:70 final size:71
Alignment explanation
Indices: 29429534--29429696 Score: 310
Period size: 70 Copynumber: 2.3 Consensus size: 71
29429524 GAGATGTATC
29429534 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
29429599 AGGACA
66 AGGACA
*
29429605 CCA-GTAGACAAGAGAGCTACATGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
29429669 AGGACA
66 AGGACA
29429675 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
29429697 AGACAAATCG
Statistics
Matches: 89, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
70 69 0.78
71 20 0.22
ACGTcount: A:0.36, C:0.18, G:0.28, T:0.18
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
AGGACA
Found at i:29436028 original size:28 final size:28
Alignment explanation
Indices: 29435982--29436050 Score: 122
Period size: 28 Copynumber: 2.5 Consensus size: 28
29435972 TTTAAAACCC
*
29435982 TAGGGGT-ATATCGGTAATTTTGCTCTT
1 TAGGGGTAATTTCGGTAATTTTGCTCTT
29436009 TAGGGGTAATTTCGGTAATTTTGCTCTT
1 TAGGGGTAATTTCGGTAATTTTGCTCTT
29436037 TAGGGGTAATTTCG
1 TAGGGGTAATTTCG
29436051 TGATCTACGC
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 7 0.17
28 33 0.82
ACGTcount: A:0.19, C:0.10, G:0.28, T:0.43
Consensus pattern (28 bp):
TAGGGGTAATTTCGGTAATTTTGCTCTT
Found at i:29437700 original size:20 final size:20
Alignment explanation
Indices: 29437677--29437714 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
29437667 CACATCCAAA
*
29437677 TACAAAATTTTAAAAATCTT
1 TACAAAATATTAAAAATCTT
*
29437697 TACAAAATATTGAAAATC
1 TACAAAATATTAAAAATC
29437715 GCGAATAAAC
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:0.53, C:0.11, G:0.03, T:0.34
Consensus pattern (20 bp):
TACAAAATATTAAAAATCTT
Found at i:29438920 original size:46 final size:48
Alignment explanation
Indices: 29438667--29438984 Score: 235
Period size: 46 Copynumber: 6.7 Consensus size: 48
29438657 GTAGAATACC
* * * * *
29438667 GATGCCATATCCCAGACATGGACTTACACTGGCTCATATCTC-AAGTT
1 GATGCCATATCCCAGACATGGTCTTACACTGGCTTACATCTCGAGGCT
* * *
29438714 GATGCCATATCCCAGACATGGTCTTACA-TTGATTATCATCATCGAGGCG
1 GATGCCATATCCCAGACATGGTCTTACACTGGCTTA-CATC-TCGAGGCT
* * * * * *
29438763 GACGCCATGTCCCAGACATGGTCTTACACTAGCTCTCACATACTTG-TGCC
1 GATGCCATATCCCAGACATGGTCTTACACTGGCT-T-ACAT-CTCGAGGCT
* * * * *
29438813 GATGCCATGTCCCAGACATGGTCTTACACTGAC--ATATCTCATAGTC-
1 GATGCCATATCCCAGACATGGTCTTACACTGGCTTACATCTC-GAGGCT
* *
29438859 GATG-CATGTCCCAGACAT-GTCTTACACTGGCTTACGTCTCGAGGCT
1 GATGCCATATCCCAGACATGGTCTTACACTGGCTTACATCTCGAGGCT
* * * *
29438905 GATG-CATATCCCAGACAT-GTCTTACACTAGCTCT-CATCTCAATGCC
1 GATGCCATATCCCAGACATGGTCTTACACTGGCT-TACATCTCGAGGCT
* * * *
29438951 AATGCCATGTCCCAGACAGGGTCTTATACTGGCT
1 GATGCCATATCCCAGACATGGTCTTACACTGGCT
29438985 CATAATAACC
Statistics
Matches: 217, Mismatches: 39, Indels: 29
0.76 0.14 0.10
Matches are distributed among these distances:
44 12 0.06
45 19 0.09
46 57 0.26
47 44 0.20
48 14 0.06
49 28 0.13
50 35 0.16
51 6 0.03
52 2 0.01
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.28
Consensus pattern (48 bp):
GATGCCATATCCCAGACATGGTCTTACACTGGCTTACATCTCGAGGCT
Found at i:29438974 original size:138 final size:145
Alignment explanation
Indices: 29438668--29438981 Score: 378
Period size: 138 Copynumber: 2.2 Consensus size: 145
29438658 TAGAATACCG
* * * *
29438668 ATGCCATATCCCAGACATGGACTTACACTGGCTCATATCTCAAGTTGATGCCATATCCCAGACAT
1 ATGCCATGTCCCAGACATGGTCTTACACT-GCACATATCTCAAGTCGATGCCATATCCCAGACAT
* *
29438733 GGTCTTACATTGATTATCATCATCGAGGCGGACGCCATGTCCCAGACATGGTCTTACACTAGCTC
65 GGTCTTACATGGATTATCATCATCGAGGCGGACGCCATATCCCAGACATGGTCTTACACTAGCTC
** *
29438798 TCACATACTTGTGCCG
130 TCACATACTAATGCCA
*
29438814 ATGCCATGTCCCAGACATGGTCTTACACTG-ACATATCTCATAGTCGATG-CATGTCCCAGACAT
1 ATGCCATGTCCCAGACATGGTCTTACACTGCACATATCTCA-AGTCGATGCCATATCCCAGACAT
* * * *
29438877 -GTCTTACACTGGCTTA-CGTC-TCGAGGCTGATG-CATATCCCAGACAT-GTCTTACACTAGCT
65 GGTCTTACA-TGGATTATCATCATCGAGGCGGACGCCATATCCCAGACATGGTCTTACACTAGCT
29438937 CT--CAT-CTCAATGCCA
129 CTCACATACT-AATGCCA
* *
29438952 ATGCCATGTCCCAGACAGGGTCTTATACTG
1 ATGCCATGTCCCAGACATGGTCTTACACTG
29438982 GCTCATAATA
Statistics
Matches: 149, Mismatches: 16, Indels: 14
0.83 0.09 0.08
Matches are distributed among these distances:
137 2 0.01
138 35 0.23
140 16 0.11
141 13 0.09
142 10 0.07
143 11 0.07
144 27 0.18
145 8 0.05
146 27 0.18
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.28
Consensus pattern (145 bp):
ATGCCATGTCCCAGACATGGTCTTACACTGCACATATCTCAAGTCGATGCCATATCCCAGACATG
GTCTTACATGGATTATCATCATCGAGGCGGACGCCATATCCCAGACATGGTCTTACACTAGCTCT
CACATACTAATGCCA
Found at i:29440324 original size:23 final size:23
Alignment explanation
Indices: 29440298--29440342 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
29440288 CCTAGAGCTA
* *
29440298 TAATTAGTGATGAAGGATCTATT
1 TAATTAGTAATGAAAGATCTATT
29440321 TAATTAGTAATGAAAGATCTAT
1 TAATTAGTAATGAAAGATCTAT
29440343 CTTTGTAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.40, C:0.04, G:0.18, T:0.38
Consensus pattern (23 bp):
TAATTAGTAATGAAAGATCTATT
Found at i:29446070 original size:8 final size:9
Alignment explanation
Indices: 29446044--29446068 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
29446034 ATGTACTTTT
29446044 AAACATTTA
1 AAACATTTA
29446053 AAACATTTA
1 AAACATTTA
29446062 AAACATT
1 AAACATT
29446069 AATTAAGGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.32
Consensus pattern (9 bp):
AAACATTTA
Found at i:29466555 original size:28 final size:28
Alignment explanation
Indices: 29466509--29466577 Score: 122
Period size: 28 Copynumber: 2.5 Consensus size: 28
29466499 TTTAAAACCC
*
29466509 TAGGGGT-ATATCGGTAATTTTGCTCTT
1 TAGGGGTAATTTCGGTAATTTTGCTCTT
29466536 TAGGGGTAATTTCGGTAATTTTGCTCTT
1 TAGGGGTAATTTCGGTAATTTTGCTCTT
29466564 TAGGGGTAATTTCG
1 TAGGGGTAATTTCG
29466578 TGATCTACGC
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 7 0.17
28 33 0.82
ACGTcount: A:0.19, C:0.10, G:0.28, T:0.43
Consensus pattern (28 bp):
TAGGGGTAATTTCGGTAATTTTGCTCTT
Found at i:29467897 original size:20 final size:20
Alignment explanation
Indices: 29467874--29467911 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
29467864 CACATCCAAA
*
29467874 TACAAAATTTTAAAAATCTT
1 TACAAAATATTAAAAATCTT
*
29467894 TACAAAATATTGAAAATC
1 TACAAAATATTAAAAATC
29467912 ACGAATAAAC
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:0.53, C:0.11, G:0.03, T:0.34
Consensus pattern (20 bp):
TACAAAATATTAAAAATCTT
Found at i:29471917 original size:37 final size:37
Alignment explanation
Indices: 29471867--29471957 Score: 164
Period size: 37 Copynumber: 2.4 Consensus size: 37
29471857 TTATTACGAA
29471867 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
1 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
29471904 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
1 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
*
29471941 GTCTCACCCGGAACATA
1 GTCTTACCCGG-ACATA
29471958 TTTCCAAGTT
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
37 47 0.90
38 5 0.10
ACGTcount: A:0.25, C:0.33, G:0.19, T:0.23
Consensus pattern (37 bp):
GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
Found at i:29472059 original size:48 final size:48
Alignment explanation
Indices: 29471997--29472100 Score: 190
Period size: 48 Copynumber: 2.2 Consensus size: 48
29471987 TGTTACAACA
*
29471997 TTCACATTAGCCATTCGGCTTTACCACACATACATATCGCACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACACATACATATCACACATATAT
*
29472045 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACACATACATATCACACATATAT
29472093 TTCACATT
1 TTCACATT
29472101 CATCACATCG
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 54 1.00
ACGTcount: A:0.32, C:0.28, G:0.07, T:0.34
Consensus pattern (48 bp):
TTCACATTAGCCATTCGGCTTTACCACACATACATATCACACATATAT
Found at i:29472149 original size:49 final size:49
Alignment explanation
Indices: 29472092--29472515 Score: 692
Period size: 49 Copynumber: 8.9 Consensus size: 49
29472082 CACACATATA
*
29472092 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACAC
1 TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATATACAC
* * *
29472141 CTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATACTC
1 TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATATACAC
*
29472188 TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATGTATATACAC
1 TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATATACAC
*
29472237 TTTCACATTCATCACATTGGCCATTAGGCCTTATCAC--ATATATACTC
1 TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATATACAC
*
29472284 TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATGTATATACAC
1 TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATATACAC
29472333 TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATAT--A-
1 TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATATACAC
29472379 ---CAC--TCATCACATTGGCCATTAGGCCTTATCACATATATATACAC
1 TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATATACAC
29472423 TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATATACAC
1 TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATATACAC
*
29472472 TTTCACATTCATCACATTGGCCATTAGGCCGTATCACATATATA
1 TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATA
29472516 CATCTCATAC
Statistics
Matches: 351, Mismatches: 12, Indels: 24
0.91 0.03 0.06
Matches are distributed among these distances:
41 37 0.11
43 4 0.01
47 93 0.26
49 217 0.62
ACGTcount: A:0.29, C:0.27, G:0.09, T:0.34
Consensus pattern (49 bp):
TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATATACAC
Found at i:29472193 original size:96 final size:96
Alignment explanation
Indices: 29472092--29472515 Score: 716
Period size: 96 Copynumber: 4.5 Consensus size: 96
29472082 CACACATATA
* *
29472092 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACCTTCACATTCATCACA
1 TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACA
*
29472157 TCGGCCATTAGGCCTTATCACATATATACTC
66 TTGGCCATTAGGCCTTATCACATATATACTC
*
29472188 TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATGTATATACACTTTCACATTCATCACA
1 TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACA
29472253 TTGGCCATTAGGCCTTATCACATATATACTC
66 TTGGCCATTAGGCCTTATCACATATATACTC
*
29472284 TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATGTATATACACTTTCACATTCATCACA
1 TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACA
29472349 TTGGCCATTAGGCCTTATCACATATATA---
66 TTGGCCATTAGGCCTTATCACATATATACTC
*
29472377 --T-ACACTCATCACATTGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACA
1 TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACA
*
29472439 TTGGCCATTAGGCCTTATCACATATATATACAC
66 TTGGCCATTAGGCCTTATCAC--ATATATACTC
*
29472472 TTTCACATTCATCACATTGGCCATTAGGCCGTATCACATATATA
1 TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATA
29472516 CATCTCATAC
Statistics
Matches: 312, Mismatches: 8, Indels: 14
0.93 0.02 0.04
Matches are distributed among these distances:
90 80 0.26
91 1 0.00
92 7 0.02
96 185 0.59
97 1 0.00
98 38 0.12
ACGTcount: A:0.29, C:0.27, G:0.09, T:0.34
Consensus pattern (96 bp):
TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACA
TTGGCCATTAGGCCTTATCACATATATACTC
Found at i:29472371 original size:22 final size:22
Alignment explanation
Indices: 29472343--29472412 Score: 62
Period size: 22 Copynumber: 3.3 Consensus size: 22
29472333 TTTCACATTC
29472343 ATCACATTGGCCATTAGGCCTT
1 ATCACATTGGCCATTAGGCCTT
*
29472365 ATCACATAT----ATATA--CACTC
1 ATCACAT-TGGCCAT-TAGGC-CTT
29472384 ATCACATTGGCCATTAGGCCTT
1 ATCACATTGGCCATTAGGCCTT
29472406 ATCACAT
1 ATCACAT
29472413 ATATATACAC
Statistics
Matches: 37, Mismatches: 2, Indels: 18
0.65 0.04 0.32
Matches are distributed among these distances:
18 2 0.05
19 11 0.30
20 2 0.05
21 2 0.05
22 18 0.49
23 2 0.05
ACGTcount: A:0.30, C:0.27, G:0.11, T:0.31
Consensus pattern (22 bp):
ATCACATTGGCCATTAGGCCTT
Found at i:29476988 original size:28 final size:28
Alignment explanation
Indices: 29476956--29477040 Score: 152
Period size: 28 Copynumber: 3.0 Consensus size: 28
29476946 GGAAAGAAAT
29476956 TTCAATTAATCAACCTAGAGTTAGTTGC
1 TTCAATTAATCAACCTAGAGTTAGTTGC
* *
29476984 TTCAATTAATCATCCTAGAGTTAATTGC
1 TTCAATTAATCAACCTAGAGTTAGTTGC
29477012 TTCAATTAATCAACCTAGAGTTAGTTGC
1 TTCAATTAATCAACCTAGAGTTAGTTGC
29477040 T
1 T
29477041 CTTACTCTCG
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 53 1.00
ACGTcount: A:0.32, C:0.18, G:0.13, T:0.38
Consensus pattern (28 bp):
TTCAATTAATCAACCTAGAGTTAGTTGC
Found at i:29477103 original size:27 final size:27
Alignment explanation
Indices: 29477065--29477121 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
29477055 AGATATTACA
29477065 ATAATTTAGGGATTTTAACGTATCAAG
1 ATAATTTAGGGATTTTAACGTATCAAG
29477092 ATAATTTAGGGATTTTAACGTATCAAG
1 ATAATTTAGGGATTTTAACGTATCAAG
29477119 ATA
1 ATA
29477122 CCAAGTGAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.39, C:0.07, G:0.18, T:0.37
Consensus pattern (27 bp):
ATAATTTAGGGATTTTAACGTATCAAG
Found at i:29478300 original size:21 final size:20
Alignment explanation
Indices: 29478274--29478312 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
29478264 TCACTTAGAA
*
29478274 AATTTTTTAAGAATGTTTTGT
1 AATTTTTTAACAAT-TTTTGT
29478295 AATTTTTTAACAATTTTT
1 AATTTTTTAACAATTTTT
29478313 AAGGACCCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.31, C:0.03, G:0.08, T:0.59
Consensus pattern (20 bp):
AATTTTTTAACAATTTTTGT
Found at i:29485381 original size:5 final size:5
Alignment explanation
Indices: 29485371--29485410 Score: 55
Period size: 5 Copynumber: 7.8 Consensus size: 5
29485361 TTATTTCTTT
29485371 TATTA TATTA TATTA TATTA -ATATA TTATTA TATTA TATT
1 TATTA TATTA TATTA TATTA TAT-TA -TATTA TATTA TATT
29485411 CTTAAATACT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
4 2 0.06
5 26 0.81
6 2 0.06
7 2 0.06
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATTA
Found at i:29491118 original size:20 final size:20
Alignment explanation
Indices: 29491093--29491139 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
29491083 ATTTTGATAT
29491093 ACATGAT-TGATATGATATGC
1 ACATGATATG-TATGATATGC
*
29491113 ACATGATATGTATTATATGC
1 ACATGATATGTATGATATGC
29491133 ACATGAT
1 ACATGAT
29491140 GTATTCATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 23 0.92
21 2 0.08
ACGTcount: A:0.36, C:0.11, G:0.17, T:0.36
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:29491218 original size:26 final size:26
Alignment explanation
Indices: 29491188--29491254 Score: 107
Period size: 26 Copynumber: 2.6 Consensus size: 26
29491178 GAGGAAGTGC
*
29491188 AAAAGGACTTATGCCCCAGTTTACCA
1 AAAAGGGCTTATGCCCCAGTTTACCA
*
29491214 AAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCA
*
29491240 AAAAGGGCTTTTGCC
1 AAAAGGGCTTATGCC
29491255 TAAGTTATTA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTACCA
Found at i:29491516 original size:31 final size:31
Alignment explanation
Indices: 29491481--29491544 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
29491471 TGTTTACAGT
29491481 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
**
29491512 AAAGGCTTCGGCCCAGTGTTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
29491543 AA
1 AA
29491545 TATGAAAAGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.38, C:0.16, G:0.23, T:0.23
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:29495649 original size:24 final size:24
Alignment explanation
Indices: 29495622--29495668 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
29495612 ATAAAGAAAG
29495622 AAATAAAATATTAAAAATGTAGTA
1 AAATAAAATATTAAAAATGTAGTA
29495646 AAATAAAATATTAAAAATGTAGT
1 AAATAAAATATTAAAAATGTAGT
29495669 GTTTTCCATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.62, C:0.00, G:0.09, T:0.30
Consensus pattern (24 bp):
AAATAAAATATTAAAAATGTAGTA
Found at i:29505170 original size:43 final size:43
Alignment explanation
Indices: 29505122--29505271 Score: 153
Period size: 43 Copynumber: 3.5 Consensus size: 43
29505112 GTTTCTGAGA
29505122 TGTGATTACATGTAAGACCATGTCTGGGACATTGGCATTGTAT
1 TGTGATTACATGTAAGACCATGTCTGGGACATTGGCATTGTAT
** *
29505165 TGTGATTAGGTGTAAGACCATGTCTGGGACATTGGCATCAT-TAA
1 TGTGATTACATGTAAGACCATGTCTGGGACATTGGCAT--TGTAT
* * * * * * *
29505209 T-CGATTTCATGTAAAACCCTGTCTGGGATAGTGGCATCG-AT
1 TGTGATTACATGTAAGACCATGTCTGGGACATTGGCATTGTAT
*
29505250 ATGTGATAACATGTAAGACCAT
1 -TGTGATTACATGTAAGACCAT
29505272 ATTTAGGATA
Statistics
Matches: 84, Mismatches: 18, Indels: 10
0.75 0.16 0.09
Matches are distributed among these distances:
41 1 0.01
42 1 0.01
43 78 0.93
44 3 0.04
45 1 0.01
ACGTcount: A:0.28, C:0.15, G:0.25, T:0.32
Consensus pattern (43 bp):
TGTGATTACATGTAAGACCATGTCTGGGACATTGGCATTGTAT
Found at i:29506703 original size:31 final size:31
Alignment explanation
Indices: 29506652--29506731 Score: 117
Period size: 31 Copynumber: 2.5 Consensus size: 31
29506642 CTCAACATGT
29506652 ACTGGGCC-ATAGCCCTTTTCATATTTCATAAC
1 ACTGGGCCGA-AG-CCTTTTCATATTTCATAAC
**
29506684 ACTGGGCCGAAGCCTTTTCATATTTCATATT
1 ACTGGGCCGAAGCCTTTTCATATTTCATAAC
29506715 ACTGGGCCGAAGCCTTT
1 ACTGGGCCGAAGCCTTT
29506732 ACTGTAAACG
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
31 34 0.76
32 10 0.22
33 1 0.02
ACGTcount: A:0.23, C:0.26, G:0.17, T:0.34
Consensus pattern (31 bp):
ACTGGGCCGAAGCCTTTTCATATTTCATAAC
Found at i:29506972 original size:25 final size:24
Alignment explanation
Indices: 29506939--29507021 Score: 123
Period size: 23 Copynumber: 3.4 Consensus size: 24
29506929 CTAGAGGCCT
29506939 AGCCTCTTTTAATAACTGGGGCAAAA
1 AGCC-CTTTTAATAACTGGGGC-AAA
*
29506965 AGCCCTTTTAATAACTGGGGCATA
1 AGCCCTTTTAATAACTGGGGCAAA
*
29506989 AGCCC-TTTAATAACTAGGGCAAA
1 AGCCCTTTTAATAACTGGGGCAAA
29507012 AGCCCTTTTA
1 AGCCCTTTTA
29507022 CACTTCCTCC
Statistics
Matches: 53, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
23 21 0.40
24 11 0.21
25 17 0.32
26 4 0.08
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.28
Consensus pattern (24 bp):
AGCCCTTTTAATAACTGGGGCAAA
Found at i:29507096 original size:20 final size:20
Alignment explanation
Indices: 29507071--29507109 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
29507061 TATGATTACA
29507071 TCATGTGCATATCATACATG
1 TCATGTGCATATCATACATG
29507091 TCATGTGCATATCATACAT
1 TCATGTGCATATCATACAT
29507110 ACCATGTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.36
Consensus pattern (20 bp):
TCATGTGCATATCATACATG
Found at i:29507115 original size:20 final size:20
Alignment explanation
Indices: 29507072--29507116 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
29507062 ATGATTACAT
**
29507072 CATGTGCATATCATACATGT
1 CATGTGCATATCATACATAC
29507092 CATGTGCATATCATACATAC
1 CATGTGCATATCATACATAC
29507112 CATGT
1 CATGT
29507117 TTATCAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.31, C:0.22, G:0.13, T:0.33
Consensus pattern (20 bp):
CATGTGCATATCATACATAC
Found at i:29514722 original size:31 final size:31
Alignment explanation
Indices: 29514671--29514750 Score: 117
Period size: 31 Copynumber: 2.5 Consensus size: 31
29514661 CTCAACATGT
29514671 ACTGGGCC-ATAGCCCTTTTCATATTTCATAAC
1 ACTGGGCCGA-AG-CCTTTTCATATTTCATAAC
**
29514703 ACTGGGCCGAAGCCTTTTCATATTTCATATT
1 ACTGGGCCGAAGCCTTTTCATATTTCATAAC
29514734 ACTGGGCCGAAGCCTTT
1 ACTGGGCCGAAGCCTTT
29514751 ACTGTAAACG
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
31 34 0.76
32 10 0.22
33 1 0.02
ACGTcount: A:0.23, C:0.26, G:0.17, T:0.34
Consensus pattern (31 bp):
ACTGGGCCGAAGCCTTTTCATATTTCATAAC
Found at i:29515005 original size:23 final size:24
Alignment explanation
Indices: 29514941--29515058 Score: 163
Period size: 23 Copynumber: 5.0 Consensus size: 24
29514931 GCTTTATCAT
*
29514941 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
*
29514966 ATAACTGGGGCAAAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
29514990 ATAACT-GGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
*
29515012 ATAACTAGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
29515035 ATAACTGGGGCATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
29515059 CACTTCCTCC
Statistics
Matches: 86, Mismatches: 4, Indels: 7
0.89 0.04 0.07
Matches are distributed among these distances:
22 10 0.12
23 45 0.52
24 19 0.22
25 12 0.14
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:29515132 original size:20 final size:20
Alignment explanation
Indices: 29515107--29515173 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
29515097 TTATGATTAC
29515107 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
29515127 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
29515147 GTCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
29515167 ACCATGT
1 ATCATGT
29515174 TTATCAAAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.34
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:29515138 original size:11 final size:11
Alignment explanation
Indices: 29515107--29515162 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
29515097 TTATGATTAC
29515107 ATCATGTGCAT
1 ATCATGTGCAT
*
29515118 ATCA--TACAT
1 ATCATGTGCAT
29515127 ATCATGTGCAT
1 ATCATGTGCAT
*
29515138 ATCA--TACAT
1 ATCATGTGCAT
*
29515147 GTCATGTGCAT
1 ATCATGTGCAT
29515158 ATCAT
1 ATCAT
29515163 ACATACCATG
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (11 bp):
ATCATGTGCAT
Found at i:29515242 original size:25 final size:25
Alignment explanation
Indices: 29515210--29515257 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
29515200 ATACATAAAC
* * *
29515210 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
29515235 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
29515258 CATGTTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:29525172 original size:42 final size:42
Alignment explanation
Indices: 29525054--29525208 Score: 159
Period size: 42 Copynumber: 3.7 Consensus size: 42
29525044 TACCATACCA
* * *
29525054 ATGCCATATCCCAGATATGGTCTTACA-TAGGATCTCGTATCG
1 ATGCCATATCCCAGATATGGTCTTACACAAAG-TCTCATATCG
* * * * **
29525096 ATGCCAATAACCCTGCTATGGTCTCACATGAAGTCTCATATCG
1 ATGCC-ATATCCCAGATATGGTCTTACACAAAGTCTCATATCG
* *
29525139 ATGCCATATCCCAGATATGGTCTTACACAAAGTCCCATATAG
1 ATGCCATATCCCAGATATGGTCTTACACAAAGTCTCATATCG
* * *
29525181 ATGTCATATCCAAGATATGGTCATACAC
1 ATGCCATATCCCAGATATGGTCTTACAC
29525209 TTAGTCTTAG
Statistics
Matches: 93, Mismatches: 18, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
42 59 0.63
43 32 0.34
44 2 0.02
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.28
Consensus pattern (42 bp):
ATGCCATATCCCAGATATGGTCTTACACAAAGTCTCATATCG
Found at i:29525677 original size:22 final size:22
Alignment explanation
Indices: 29525652--29525693 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
29525642 CCATATTTTT
*
29525652 CATTTAATTACATTTTTACACA
1 CATTTAATAACATTTTTACACA
*
29525674 CATTTAATAACCTTTTTACA
1 CATTTAATAACATTTTTACA
29525694 AATTGGTCCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.36, C:0.19, G:0.00, T:0.45
Consensus pattern (22 bp):
CATTTAATAACATTTTTACACA
Found at i:29529672 original size:4 final size:4
Alignment explanation
Indices: 29529663--29529742 Score: 74
Period size: 4 Copynumber: 19.0 Consensus size: 4
29529653 CTAAATGAGG
* *
29529663 TAAA TAAA TAAA TGATA TAATCA TAAA CAAA -ATAA TAGAA TAAAA TAAA
1 TAAA TAAA TAAA T-AAA TAA--A TAAA TAAA TA-AA TA-AA T-AAA TAAA
29529712 TAAA TAAA TAAA TAAA TAAA TAAA T-AA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
29529743 ATAGGAAAAT
Statistics
Matches: 65, Mismatches: 4, Indels: 14
0.78 0.05 0.17
Matches are distributed among these distances:
3 4 0.06
4 46 0.71
5 10 0.15
6 5 0.08
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.25
Consensus pattern (4 bp):
TAAA
Found at i:29534644 original size:41 final size:41
Alignment explanation
Indices: 29534586--29534668 Score: 132
Period size: 41 Copynumber: 2.0 Consensus size: 41
29534576 ATGTTACTTT
29534586 TATAGGTTATCACGTACCCAA-CGAAGGATGGACTAGATCTA
1 TATAGGTTATCACGTACCCAAGCGAA-GATGGACTAGATCTA
* *
29534627 TATAGGTTATCATGTACCCAAGGGAAGATGGACTAGATCTA
1 TATAGGTTATCACGTACCCAAGCGAAGATGGACTAGATCTA
29534668 T
1 T
29534669 TGAAAACTTC
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
41 36 0.92
42 3 0.08
ACGTcount: A:0.34, C:0.17, G:0.23, T:0.27
Consensus pattern (41 bp):
TATAGGTTATCACGTACCCAAGCGAAGATGGACTAGATCTA
Found at i:29538602 original size:48 final size:46
Alignment explanation
Indices: 29538501--29538764 Score: 238
Period size: 48 Copynumber: 5.6 Consensus size: 46
29538491 GATATTGTGT
* * *
29538501 GCTAGTGTAAGA-CATGTTTGGGACAT-GCATCAGCCACATTA-TGAGA
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATC-G--ACATAAGAGAGA
*
29538547 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGACATTAAGACGAGA
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGACA-TAAGA-GAGA
* * * *
29538595 GCTAGTGTAAGA-CATGTCCGGGACAT-GCATCGGC-TACGAGATGT
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGACATAAGAGA-GA
* *
29538639 GATAGTGTAAGACCATGTCTGGGACATGGCATCGACACGTATAGAG-GT
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGACA--TA-AGAGAGA
* *
29538687 G-TCAGTGTAAGACCATGTCTGGGATATGGCATCGACATAGATATGTAAGA
1 GCT-AGTGTAAGACCATGTCTGGGACATGGCATCGACATA-AGA-G--AGA
29538737 GCTAGTGTAAGACCATGTCTGGGACATG
1 GCTAGTGTAAGACCATGTCTGGGACATG
29538765 TCGTCGGCCT
Statistics
Matches: 182, Mismatches: 18, Indels: 32
0.78 0.08 0.14
Matches are distributed among these distances:
43 2 0.01
44 16 0.09
45 16 0.09
46 31 0.17
47 29 0.16
48 56 0.31
49 2 0.01
50 29 0.16
51 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.30, T:0.23
Consensus pattern (46 bp):
GCTAGTGTAAGACCATGTCTGGGACATGGCATCGACATAAGAGAGA
Found at i:29538670 original size:92 final size:93
Alignment explanation
Indices: 29538501--29538764 Score: 288
Period size: 94 Copynumber: 2.8 Consensus size: 93
29538491 GATATTGTGT
* * * * *
29538501 GCTAGTGTAAGACATGTTTGGGACATGCATCAGCCAC-ATTATGAGAGCCAGTGTAAGACCATGT
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCTACGA-TATGTGA-CTAGTGTAAGACCATGT
*
29538565 CTGGGACATGGCATCGACA-TTA-AGACGAGA
64 CTGGGACATGGCATCGACACGTATAGA-G-GA
* *
29538595 GCTAGTGTAAGACATGTCCGGGACATGCATCGGCTACGAGATGTGA-TAGTGTAAGACCATGTCT
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCTACGATATGTGACTAGTGTAAGACCATGTCT
*
29538659 GGGACATGGCATCGACACGTATAGAGGT
66 GGGACATGGCATCGACACGTATAGAGGA
* *
29538687 G-TCAGTGTAAGACCATGTCTGGGATATGGCATCGACATA-GATATGTAAGAGCTAGTGTAAGAC
1 GCT-AGTGTAAGA-CATGTCTGGGACAT-GCATCGGC-TACGATATGT--GA-CTAGTGTAAGAC
29538750 CATGTCTGGGACATG
59 CATGTCTGGGACATG
29538765 TCGTCGGCCT
Statistics
Matches: 146, Mismatches: 13, Indels: 18
0.82 0.07 0.10
Matches are distributed among these distances:
91 1 0.01
92 45 0.31
93 15 0.10
94 54 0.37
95 3 0.02
96 2 0.01
98 26 0.18
ACGTcount: A:0.29, C:0.18, G:0.30, T:0.23
Consensus pattern (93 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCGGCTACGATATGTGACTAGTGTAAGACCATGTCT
GGGACATGGCATCGACACGTATAGAGGA
Found at i:29538820 original size:147 final size:140
Alignment explanation
Indices: 29538503--29538871 Score: 362
Period size: 140 Copynumber: 2.6 Consensus size: 140
29538493 TATTGTGTGC
* * * * *
29538503 TAGTGTAAGA-CATGTTTGGGACAT-GCATCAGCCACAT-TATGA-GAGCCAGTGTAAGACCATG
1 TAGTGTAAGACCATGTCTGGGACATGGCATC-GACACGTATA-GAGGTGTCAGTGTAAGACCATG
29538564 TCTGGGACATGGCATCGACATTAAGACGAGAGCTAGTGTAAGACATGTCCGGGACATGCATCGGC
64 TCTGGGACATGGCATCGACATTAAGACGAGAGCTAGTGTAAGACATGTCCGGGACATGCATCGGC
* *
29538629 TACGAGATGTGA
129 TACGAAATGTCA
29538641 TAGTGTAAGACCATGTCTGGGACATGGCATCGACACGTATAGAGGTGTCAGTGTAAGACCATGTC
1 TAGTGTAAGACCATGTCTGGGACATGGCATCGACACGTATAGAGGTGTCAGTGTAAGACCATGTC
* * * * *
29538706 TGGGATATGGCATCGACA-TAGATATGTAAGAGCTAGTGTAAGACCATGTCTGGGACATGTCGTC
66 TGGGACATGGCATCGACATTA-AGACG--AGAGCTAGTGTAAGA-CATGTCCGGGACATG-CATC
29538770 GGCCT-CGATTTCAATAGTCA
126 GG-CTACGA----AAT-GTCA
** * * * * *
29538790 -A-TGTAAGACCATGTCTGGGACATGGCATCGACTTG-ATGGATGAGCCAGTGTAAG-CCATGCC
1 TAGTGTAAGACCATGTCTGGGACATGGCATCGACACGTATAGAGGTGTCAGTGTAAGACCATGTC
* *
29538851 TAGGACATGGCATCGGCATTA
66 TGGGACATGGCATCGACATTA
29538872 TACCCTATGT
Statistics
Matches: 193, Mismatches: 22, Indels: 24
0.81 0.09 0.10
Matches are distributed among these distances:
138 10 0.05
139 22 0.11
140 46 0.24
142 15 0.08
143 14 0.07
144 8 0.04
145 23 0.12
146 17 0.09
147 32 0.17
148 3 0.02
149 3 0.02
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.24
Consensus pattern (140 bp):
TAGTGTAAGACCATGTCTGGGACATGGCATCGACACGTATAGAGGTGTCAGTGTAAGACCATGTC
TGGGACATGGCATCGACATTAAGACGAGAGCTAGTGTAAGACATGTCCGGGACATGCATCGGCTA
CGAAATGTCA
Found at i:29545663 original size:47 final size:47
Alignment explanation
Indices: 29545452--29545678 Score: 195
Period size: 48 Copynumber: 4.7 Consensus size: 47
29545442 GAGATGTGTT
* * * * *
29545452 AGTGTAATACCATGTCTGGGACATGGCATCGACACGTATAGAGGTGTC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGACTCG-ATAGATGAGCC
* * * * * *
29545500 AGTTTAAGACCATGTCTGGGACATGGCATTGGCACGGATATGTAAGAGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGACTC-GATA-G-ATGAGCC
* * * * * *
29545550 AGTGTAAGACCATGTCCGGGACATGTCGTCGGCCTCGATTTCGAT-AGTC
1 AGTGTAAGACCATGTCTGGGACATGGCATC-GACTCGA--TAGATGAGCC
* * *
29545599 AATGTAAGACCATGTCTAGGACATGGCATCGACTTGATAGATGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGACTCGATAGATGAGCC
*
29545646 AGTGTAAGACCATGTCTAGGACATGGCATCGAC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGAC
29545679 ATTATACCCT
Statistics
Matches: 143, Mismatches: 29, Indels: 15
0.76 0.16 0.08
Matches are distributed among these distances:
46 4 0.03
47 35 0.24
48 39 0.27
49 29 0.20
50 31 0.22
51 4 0.03
52 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.28, T:0.25
Consensus pattern (47 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGACTCGATAGATGAGCC
Found at i:29555852 original size:24 final size:24
Alignment explanation
Indices: 29555825--29555881 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
29555815 AAGCCTAATT
*
29555825 CTAATCAATG-TAAATTATATTATG
1 CTAATAAATGCTAAA-TATATTATG
*
29555849 CTAATAAATGCTAAATATATTATA
1 CTAATAAATGCTAAATATATTATG
*
29555873 CTACTAAAT
1 CTAATAAAT
29555882 CTTTCAGAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 25 0.86
25 4 0.14
ACGTcount: A:0.46, C:0.11, G:0.05, T:0.39
Consensus pattern (24 bp):
CTAATAAATGCTAAATATATTATG
Found at i:29559315 original size:26 final size:26
Alignment explanation
Indices: 29559263--29559313 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 26
29559253 AAATTTTAAA
*
29559263 TAAAATAAATATCTCTAGAAATTTTC
1 TAAAATAAATATCTCAAGAAATTTTC
29559289 TAAAAT-AATATCTTCAAAGAAATTT
1 TAAAATAAATATC-TC-AAGAAATTT
29559314 CTCTCTACAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 6 0.27
26 8 0.36
27 8 0.36
ACGTcount: A:0.49, C:0.10, G:0.04, T:0.37
Consensus pattern (26 bp):
TAAAATAAATATCTCAAGAAATTTTC
Found at i:29559567 original size:20 final size:18
Alignment explanation
Indices: 29559517--29559568 Score: 54
Period size: 20 Copynumber: 2.8 Consensus size: 18
29559507 CTACAAGATA
29559517 AATATTAAATTAA-ATTT
1 AATATTAAATTAATATTT
*
29559534 AAAATTAAGA-TAATCACTTT
1 AATATTAA-ATTAAT-A-TTT
29559554 AATATTAAATTAATA
1 AATATTAAATTAATA
29559569 AAATACTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
17 10 0.36
18 1 0.04
19 3 0.11
20 14 0.50
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (18 bp):
AATATTAAATTAATATTT
Found at i:29569103 original size:71 final size:71
Alignment explanation
Indices: 29569015--29569249 Score: 470
Period size: 71 Copynumber: 3.3 Consensus size: 71
29569005 CGATTTGTCT
29569015 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
29569080 CTTTCA
66 CTTTCA
29569086 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
29569151 CTTTCA
66 CTTTCA
29569157 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
29569222 CTTTCA
66 CTTTCA
29569228 CGTAGCTCTCTTGTCTACATGG
1 CGTAGCTCTCTTGTCTACATGG
29569250 GATACATCTC
Statistics
Matches: 164, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 164 1.00
ACGTcount: A:0.19, C:0.28, G:0.17, T:0.35
Consensus pattern (71 bp):
CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
CTTTCA
Found at i:29569145 original size:41 final size:41
Alignment explanation
Indices: 29569100--29569217 Score: 98
Period size: 41 Copynumber: 3.1 Consensus size: 41
29569090 GCTCTCTTGT
29569100 CTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAG
1 CTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAG
* * * * *
29569141 CTACAT-TTATCTTTCAC---G--T-A-GC-T-C--TCTTG
1 CTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAG
29569170 TCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAG
1 -CTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAG
29569212 CTACAT
1 CTACAT
29569218 TTATCTTTCA
Statistics
Matches: 54, Mismatches: 10, Indels: 26
0.60 0.11 0.29
Matches are distributed among these distances:
29 3 0.06
30 6 0.11
31 9 0.17
32 1 0.02
33 2 0.04
34 2 0.04
35 1 0.02
36 1 0.02
37 2 0.04
38 2 0.04
39 1 0.02
40 9 0.17
41 12 0.22
42 3 0.06
ACGTcount: A:0.21, C:0.29, G:0.18, T:0.32
Consensus pattern (41 bp):
CTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAG
Found at i:29569287 original size:142 final size:141
Alignment explanation
Indices: 29569015--29569283 Score: 454
Period size: 142 Copynumber: 1.9 Consensus size: 141
29569005 CGATTTGTCT
29569015 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
* * *
29569080 CTTTCACGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTAC
66 CTTTCACGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACGCATGCGACCTAGCTAC
29569145 ATTTATCTTTCA
130 ATTTATCTTTCA
29569157 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
* *
29569222 CTTTCACGTAGCTCTCTTGTCTACATGG-GATACAT-C-TCGTATCACGCATGTGACCTAGCTAC
66 CTTTCACGTAGCTCTCTTGTCTACATGGTG-TACATACTTCGAATCACGCATGCGACCTAGCTAC
29569284 TACAGGGTGT
Statistics
Matches: 121, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
139 23 0.19
140 1 0.01
141 1 0.01
142 96 0.79
ACGTcount: A:0.20, C:0.28, G:0.17, T:0.34
Consensus pattern (141 bp):
CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
CTTTCACGTAGCTCTCTTGTCTACATGGTGTACATACTTCGAATCACGCATGCGACCTAGCTACA
TTTATCTTTCA
Found at i:29575213 original size:19 final size:19
Alignment explanation
Indices: 29575168--29575214 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
29575158 ATCAAATTAA
*
29575168 AATAAAAATAAAAATATAG
1 AATAAAAATAAAAATAAAG
* *
29575187 AATCAAAACT-AAAATAAAT
1 AAT-AAAAATAAAAATAAAG
29575206 AATAAAAAT
1 AATAAAAAT
29575215 TAGAGTAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 5 0.22
19 13 0.57
20 5 0.22
ACGTcount: A:0.72, C:0.04, G:0.02, T:0.21
Consensus pattern (19 bp):
AATAAAAATAAAAATAAAG
Found at i:29580070 original size:31 final size:31
Alignment explanation
Indices: 29580035--29580098 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
29580025 TCTTTTCATG
29580035 TTTCATATTCCATAACACTGGGCCGAAGCCT
1 TTTCATATTCCATAACACTGGGCCGAAGCCT
* **
29580066 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTCCATAACACTGGGCCGAAGCCT
29580097 TT
1 TT
29580099 ACTGTAAACG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.23, C:0.25, G:0.16, T:0.36
Consensus pattern (31 bp):
TTTCATATTCCATAACACTGGGCCGAAGCCT
Found at i:29580341 original size:24 final size:24
Alignment explanation
Indices: 29580290--29580480 Score: 305
Period size: 24 Copynumber: 8.0 Consensus size: 24
29580280 GCTTTATCAT
* *
29580290 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTG
* **
29580315 ATAACTGGGGCAAAAGCCCTTTCA
1 ATAACTGGGGCATAAGCCCTTTTG
29580339 ATAACTGGGGCATAAGCCCTTTT-
1 ATAACTGGGGCATAAGCCCTTTTG
29580362 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTG
29580386 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTG
29580410 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTG
29580434 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTG
29580458 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
29580481 TCACTTCCTC
Statistics
Matches: 159, Mismatches: 5, Indels: 5
0.94 0.03 0.03
Matches are distributed among these distances:
23 23 0.14
24 124 0.78
25 12 0.08
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.29
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTG
Found at i:29580555 original size:20 final size:20
Alignment explanation
Indices: 29580530--29580590 Score: 104
Period size: 20 Copynumber: 3.0 Consensus size: 20
29580520 TTATGATTAC
29580530 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
29580550 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
* *
29580570 GTCATGTGCATCTCATACAT
1 ATCATGTGCATATCATACAT
29580590 A
1 A
29580591 CCATATTTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.33, C:0.21, G:0.11, T:0.34
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:29580665 original size:25 final size:25
Alignment explanation
Indices: 29580633--29580680 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
29580623 ATACATAAAC
* * *
29580633 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
29580658 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
29580681 CATGGTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:29584368 original size:42 final size:42
Alignment explanation
Indices: 29584322--29584401 Score: 108
Period size: 42 Copynumber: 1.9 Consensus size: 42
29584312 GCGTTTCCAC
*
29584322 TAAAAACGCCATTATAGT-TTAACTTTTTACGGCATTTTTTTA
1 TAAAAACACCATTATA-TCTTAACTTTTTACGGCATTTTTTTA
* **
29584364 TAAAAACACCATTATATCTTAATTTTTTGTGGCATTTT
1 TAAAAACACCATTATATCTTAACTTTTTACGGCATTTT
29584402 ACCTAAAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
41 1 0.03
42 32 0.97
ACGTcount: A:0.31, C:0.14, G:0.09, T:0.46
Consensus pattern (42 bp):
TAAAAACACCATTATATCTTAACTTTTTACGGCATTTTTTTA
Found at i:29584479 original size:9 final size:9
Alignment explanation
Indices: 29584434--29584480 Score: 58
Period size: 9 Copynumber: 5.0 Consensus size: 9
29584424 TTAATTTTAA
*
29584434 ATTTTTTAT
1 ATTTTTTCT
*
29584443 ATTTTTAACAT
1 ATTTTT-TC-T
29584454 ATTTTTTCT
1 ATTTTTTCT
29584463 ATTTTTTCT
1 ATTTTTTCT
29584472 ATTTTTTCT
1 ATTTTTTCT
29584481 TTCAAATTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
9 25 0.76
10 1 0.03
11 7 0.21
ACGTcount: A:0.19, C:0.09, G:0.00, T:0.72
Consensus pattern (9 bp):
ATTTTTTCT
Found at i:29586042 original size:27 final size:26
Alignment explanation
Indices: 29586012--29586074 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 26
29586002 TTTTTATTTT
29586012 TATTTATTTATAAAT-TACATATTATTA
1 TATTTA-TTATAAATATA-ATATTATTA
*
29586039 TATTGTATTATATATATAATATTATTA
1 TATT-TATTATAAATATAATATTATTA
29586066 TATTT-TTAT
1 TATTTATTAT
29586075 TATGTATTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
25 4 0.12
26 1 0.03
27 24 0.73
28 4 0.12
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (26 bp):
TATTTATTATAAATATAATATTATTA
Found at i:29586075 original size:14 final size:14
Alignment explanation
Indices: 29585986--29586077 Score: 51
Period size: 14 Copynumber: 7.1 Consensus size: 14
29585976 TGTAACATTC
29585986 ATTATA-TTATATT
1 ATTATATTTATATT
29585999 ATT-T-TTT-TATT
1 ATTATATTTATATT
29586010 -TT-TATTTAT-TT
1 ATTATATTTATATT
* *
29586021 A-TAAATTACATATT
1 ATTATATT-TATATT
*
29586035 ATTATA-TTGTATT
1 ATTATATTTATATT
*
29586048 A-TATATATAATATT
1 ATTATAT-TTATATT
*
29586062 ATTATATTTTTATT
1 ATTATATTTATATT
29586076 AT
1 AT
29586078 GTATTATTAC
Statistics
Matches: 59, Mismatches: 9, Indels: 21
0.66 0.10 0.24
Matches are distributed among these distances:
10 3 0.05
11 10 0.17
12 11 0.19
13 10 0.17
14 17 0.29
15 8 0.14
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.63
Consensus pattern (14 bp):
ATTATATTTATATT
Found at i:29588515 original size:24 final size:24
Alignment explanation
Indices: 29588488--29588536 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
29588478 CCAAAATAAC
29588488 AATTAATTTTTATATAAACTTTTA
1 AATTAATTTTTATATAAACTTTTA
29588512 AATTAATTTTTATATAAACTTTTA
1 AATTAATTTTTATATAAACTTTTA
29588536 A
1 A
29588537 TAAATATATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (24 bp):
AATTAATTTTTATATAAACTTTTA
Found at i:29588539 original size:11 final size:12
Alignment explanation
Indices: 29588495--29588540 Score: 58
Period size: 12 Copynumber: 3.9 Consensus size: 12
29588485 AACAATTAAT
29588495 TTTTATATAAAC
1 TTTTATATAAAC
* * *
29588507 TTTTAAATTAAT
1 TTTTATATAAAC
29588519 TTTTATATAAAC
1 TTTTATATAAAC
29588531 TTTTA-ATAAA
1 TTTTATATAAA
29588541 TATATGAGTT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
11 5 0.18
12 23 0.82
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.52
Consensus pattern (12 bp):
TTTTATATAAAC
Found at i:29589196 original size:41 final size:40
Alignment explanation
Indices: 29589149--29589326 Score: 209
Period size: 41 Copynumber: 4.4 Consensus size: 40
29589139 GTTATATAAC
*
29589149 TTTTAGCGGTGTTTTACCAAAAACGCCGCTAATGCCCTCTT
1 TTTTAGCGGCGTTTTACCAAAAACGCCGCTAATG-CCTCTT
* *
29589190 TTTTAGCGGCGTTTTACCAAAAGCGCTGCTAATG-CTCTGGT
1 TTTTAGCGGCGTTTTACCAAAAACGCCGCTAATGCCTCT--T
*
29589231 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATG-CTCTGT
1 TTTTAGCGGCGTTTTACCAAAAACGCCGCTAATGCCTCT-T
* * * *
29589271 TTTTAGCGGCGTTTTAACAAAAAACGCCGTTATTG-CTCAAT
1 TTTTAGCGGCGTTTT-ACCAAAAACGCCGCTAATGCCTC-TT
29589312 TTTTAGCGGCGTTTT
1 TTTTAGCGGCGTTTT
29589327 TGTTAAAACG
Statistics
Matches: 124, Mismatches: 9, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
39 4 0.03
40 17 0.14
41 103 0.83
ACGTcount: A:0.21, C:0.22, G:0.21, T:0.35
Consensus pattern (40 bp):
TTTTAGCGGCGTTTTACCAAAAACGCCGCTAATGCCTCTT
Found at i:29589322 original size:81 final size:81
Alignment explanation
Indices: 29589149--29589326 Score: 234
Period size: 82 Copynumber: 2.2 Consensus size: 81
29589139 GTTATATAAC
* * *
29589149 TTTTAGCGGTGTTTTACCAAAAACGCCGCTAATGCCCTCTTTTTTAGCGGCGTTTTACCAAAAGC
1 TTTTAGCGGCGTTTTACCAAAAACGCCGCTAATG-CCTCTTTTTTAGCGGCGTTTTACAAAAAAC
* **
29589214 GCTGCTAATGCTCTGGT
65 GCCGCTAATGCTCTAAT
*
29589231 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATG-CTCTGTTTTTAGCGGCGTTTTAACAAAAAA
1 TTTTAGCGGCGTTTTACCAAAAACGCCGCTAATGCCTCT-TTTTTAGCGGCGTTTT-ACAAAAAA
* *
29589295 CGCCGTTATTGCTC-AAT
64 CGCCGCTAATGCTCTAAT
29589312 TTTTAGCGGCGTTTT
1 TTTTAGCGGCGTTTT
29589327 TGTTAAAACG
Statistics
Matches: 85, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
80 4 0.05
81 32 0.38
82 49 0.58
ACGTcount: A:0.21, C:0.22, G:0.21, T:0.35
Consensus pattern (81 bp):
TTTTAGCGGCGTTTTACCAAAAACGCCGCTAATGCCTCTTTTTTAGCGGCGTTTTACAAAAAACG
CCGCTAATGCTCTAAT
Found at i:29589357 original size:41 final size:41
Alignment explanation
Indices: 29589149--29589357 Score: 131
Period size: 41 Copynumber: 5.1 Consensus size: 41
29589139 GTTATATAAC
* * ** *
29589149 TTTTAGCGGTGTTTT-ACCAAAAACGCCGCTAATGCCCTCT-T
1 TTTTAGCGGCGTTTTAACAAAAAACGCCATTACTG--CTCTGT
* * *** *
29589190 TTTTAGCGGCGTTTT-ACCAAAAGCGCTGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTAACAAAAAACGCCATTACTGCTCT-GT
* * ** *
29589231 TTTTAGCGGCGTTTT-ACCAAAAGCGCCGCTAATGCTCTGT
1 TTTTAGCGGCGTTTTAACAAAAAACGCCATTACTGCTCTGT
* * **
29589271 TTTTAGCGGCGTTTTAACAAAAAACGCCGTTATTGCTCAAT
1 TTTTAGCGGCGTTTTAACAAAAAACGCCATTACTGCTCTGT
****
29589312 TTTTAGCGGCGTTTT-TGTTAAAACGCCATTACTGCTCTGT
1 TTTTAGCGGCGTTTTAACAAAAAACGCCATTACTGCTCTGT
29589352 GTTTTA
1 -TTTTA
29589358 CAATTTTTGC
Statistics
Matches: 146, Mismatches: 18, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
39 4 0.03
40 34 0.23
41 108 0.74
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.36
Consensus pattern (41 bp):
TTTTAGCGGCGTTTTAACAAAAAACGCCATTACTGCTCTGT
Found at i:29591983 original size:1 final size:1
Alignment explanation
Indices: 29591972--29592016 Score: 54
Period size: 1 Copynumber: 45.0 Consensus size: 1
29591962 GACCACTAGA
* * * *
29591972 TTTTTTATTTTTTTATTTTTTTTTTTTTTTTTATTTTTATTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
29592017 ATGTGTAAGC
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
1 36 1.00
ACGTcount: A:0.09, C:0.00, G:0.00, T:0.91
Consensus pattern (1 bp):
T
Found at i:29591985 original size:8 final size:8
Alignment explanation
Indices: 29591972--29592016 Score: 65
Period size: 8 Copynumber: 5.6 Consensus size: 8
29591962 GACCACTAGA
29591972 TTTTTTAT
1 TTTTTTAT
29591980 TTTTTTAT
1 TTTTTTAT
29591988 TTTTTT-T
1 TTTTTTAT
*
29591995 TTTTTTTT
1 TTTTTTAT
29592003 TATTTTTAT
1 T-TTTTTAT
29592012 TTTTT
1 TTTTT
29592017 ATGTGTAAGC
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
7 7 0.21
8 20 0.59
9 7 0.21
ACGTcount: A:0.09, C:0.00, G:0.00, T:0.91
Consensus pattern (8 bp):
TTTTTTAT
Found at i:29592015 original size:18 final size:18
Alignment explanation
Indices: 29591974--29592016 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 18
29591964 CCACTAGATT
*
29591974 TTTTATTTTTTTATTTTTT
1 TTTT-TTTTTTTATTTTTA
29591993 TTTTTTTTTTTATTTTTA
1 TTTTTTTTTTTATTTTTA
29592011 TTTTTT
1 TTTTTT
29592017 ATGTGTAAGC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 19 0.83
19 4 0.17
ACGTcount: A:0.09, C:0.00, G:0.00, T:0.91
Consensus pattern (18 bp):
TTTTTTTTTTTATTTTTA
Found at i:29594192 original size:22 final size:25
Alignment explanation
Indices: 29594166--29594212 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
29594156 GTTGAAATTT
29594166 TGAAAA-AT-AAA-AATAAAATATA
1 TGAAAAGATAAAACAATAAAATATA
29594188 TGAAAAGTATAAAACAATAAAATAT
1 TGAAAAG-ATAAAACAATAAAATAT
29594213 TGTTTTCACT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
22 6 0.29
24 2 0.10
25 3 0.14
26 10 0.48
ACGTcount: A:0.68, C:0.02, G:0.06, T:0.23
Consensus pattern (25 bp):
TGAAAAGATAAAACAATAAAATATA
Found at i:29596263 original size:26 final size:26
Alignment explanation
Indices: 29596230--29596289 Score: 93
Period size: 26 Copynumber: 2.3 Consensus size: 26
29596220 TATTTATTTA
*
29596230 TTTATTTTCTTGATTTCTATATATAT
1 TTTATTTTCTAGATTTCTATATATAT
* *
29596256 TTTATTTTCTAGATTTCTATTTCTAT
1 TTTATTTTCTAGATTTCTATATATAT
29596282 TTTATTTT
1 TTTATTTT
29596290 ATTATGCATT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.20, C:0.08, G:0.03, T:0.68
Consensus pattern (26 bp):
TTTATTTTCTAGATTTCTATATATAT
Found at i:29598351 original size:27 final size:26
Alignment explanation
Indices: 29598312--29598444 Score: 99
Period size: 27 Copynumber: 5.0 Consensus size: 26
29598302 GCGAGGTTGC
* *
29598312 CAGATATTGTGAC-GAAGTCACCAGATA
1 CAGATATTCTGACAG-AGCCACCAGA-A
29598339 CAGATATTCTGACAGAGCCACCAGAA
1 CAGATATTCTGACAGAGCCACCAGAA
* * *
29598365 CAGATATATGTGGCAGAGCCACCAGAT
1 CAGATAT-TCTGACAGAGCCACCAGAA
* * * *
29598392 CAGATAATTGTGGCATAACCACCA-AGA
1 CAGAT-ATTCTGACAGAGCCACCAGA-A
* *
29598419 CAGATATATGTGGCAGAGCCACCAGA
1 CAGATAT-TCTGACAGAGCCACCAGA
29598445 TCAAATAATT
Statistics
Matches: 90, Mismatches: 10, Indels: 11
0.81 0.09 0.10
Matches are distributed among these distances:
26 11 0.12
27 75 0.83
28 4 0.04
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.18
Consensus pattern (26 bp):
CAGATATTCTGACAGAGCCACCAGAA
Found at i:29598414 original size:54 final size:55
Alignment explanation
Indices: 29598330--29598470 Score: 207
Period size: 54 Copynumber: 2.6 Consensus size: 55
29598320 GTGACGAAGT
* * *
29598330 CACCAGATACAGAT-ATTCTGACAGAGCCACCAGA-ACAGATATATGTGGCAGAGC
1 CACCAGAT-CAGATAATTGTGGCATAGCCACCAGAGACAGATATATGTGGCAGAGC
*
29598384 CACCAGATCAGATAATTGTGGCATAACCACCA-AGACAGATATATGTGGCAGAGC
1 CACCAGATCAGATAATTGTGGCATAGCCACCAGAGACAGATATATGTGGCAGAGC
*
29598438 CACCAGATCAAATAATTGTGGCATAGCCACCAG
1 CACCAGATCAGATAATTGTGGCATAGCCACCAG
29598471 GACGCTTCCT
Statistics
Matches: 78, Mismatches: 6, Indels: 5
0.88 0.07 0.06
Matches are distributed among these distances:
53 6 0.08
54 72 0.92
ACGTcount: A:0.37, C:0.24, G:0.21, T:0.18
Consensus pattern (55 bp):
CACCAGATCAGATAATTGTGGCATAGCCACCAGAGACAGATATATGTGGCAGAGC
Done.