Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr1
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: 37323695
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 1370832 characters in sequence are not A, C, G, or T
File 75 of 93
Found at i:28880828 original size:2 final size:2
Alignment explanation
Indices: 28880821--28880908 Score: 84
Period size: 2 Copynumber: 47.0 Consensus size: 2
28880811 TGTGGTGTTC
28880821 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA T- TA -A T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
28880859 TA TT TA T- TA T- TA CT- TNC TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA -TA T-A TA TA TA TA TA TA TA TA TA TA TA TA
28880900 TA TA T- TA TA
1 TA TA TA TA TA
28880909 GTTAAATATT
Statistics
Matches: 73, Mismatches: 3, Indels: 20
0.76 0.03 0.21
Matches are distributed among these distances:
1 8 0.11
2 63 0.86
3 2 0.03
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:28880906 original size:57 final size:56
Alignment explanation
Indices: 28880821--28880928 Score: 173
Period size: 57 Copynumber: 1.9 Consensus size: 56
28880811 TGTGGTGTTC
*
28880821 TATATATATATATATATATATATATATTATATATTAATTA-TTTATTATTACTTNCTA
1 TATATATATATATATATATATATATATTATA-ATTAAATATTTTATTATTACTT-CTA
*
28880878 TATATATATATATATATATATATATATTATAGTTAAATATTTTATTATTAC
1 TATATATATATATATATATATATATATTATAATTAAATATTTTATTATTAC
28880929 CTTGTTATAT
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
56 6 0.12
57 42 0.88
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.54
Consensus pattern (56 bp):
TATATATATATATATATATATATATATTATAATTAAATATTTTATTATTACTTCTA
Found at i:28881373 original size:19 final size:19
Alignment explanation
Indices: 28881346--28881391 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
28881336 TGCCCCCGCT
*
28881346 TTTTCTTTTCTATTTTTTC
1 TTTTCTTTTCTATTCTTTC
* * *
28881365 TTTTGTTTTTTCTTCTTTC
1 TTTTCTTTTCTATTCTTTC
28881384 TTTTCTTT
1 TTTTCTTT
28881392 GTTTTCTTTC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.02, C:0.15, G:0.02, T:0.80
Consensus pattern (19 bp):
TTTTCTTTTCTATTCTTTC
Found at i:28881391 original size:9 final size:9
Alignment explanation
Indices: 28881346--28881401 Score: 51
Period size: 9 Copynumber: 6.0 Consensus size: 9
28881336 TGCCCCCGCT
28881346 TTTTCTTTTC
1 TTTTC-TTTC
28881356 TATTT-TTTC
1 T-TTTCTTTC
* *
28881365 TTTTGTTTT
1 TTTTCTTTC
28881374 TTCTTCTTTC
1 TT-TTCTTTC
*
28881384 TTTTCTTTG
1 TTTTCTTTC
28881393 TTTTCTTTC
1 TTTTCTTTC
28881402 CCACTTCTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
8 3 0.08
9 24 0.63
10 8 0.21
11 3 0.08
ACGTcount: A:0.02, C:0.16, G:0.04, T:0.79
Consensus pattern (9 bp):
TTTTCTTTC
Found at i:28892006 original size:2 final size:2
Alignment explanation
Indices: 28891999--28892049 Score: 77
Period size: 2 Copynumber: 26.0 Consensus size: 2
28891989 TATAAATTAA
* *
28891999 AT AT AT AT AT AT AT A- AT GT TT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28892040 AT AT AT AT AT
1 AT AT AT AT AT
28892050 TCATAACATT
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
AT
Found at i:28892097 original size:202 final size:202
Alignment explanation
Indices: 28891675--28892037 Score: 485
Period size: 202 Copynumber: 1.8 Consensus size: 202
28891665 TCAAAGTTTG
* *
28891675 TATAAATAATAACTAATTAT-AA-A-TATGTAATAAAAATTAAAGTGATAACTAATAAAATTATT
1 TATAAATAATAATTAATTATAAACAGTATGTAATAAAAACTAAAGTGATAACTAATAAAATTATT
* *
28891737 AAGTGTAATCATATAAATAAAGTCTATTATAAGTTATAGTAATGTTTATGTATAAATTAAACATA
66 AAGTGTAATCATATAAATAAAATCTATTATAAATTATAGTAATGTTTATGTATAAATTAAACATA
* * * *
28891802 CGTATGTATATATAATATATTACTTTATTATGTATATATGAAACTAATGACACAACTTTAAATCA
131 CATATATATATATAATATATTACTATATTATATATATATGAAACTAATGACACAACTTTAAATCA
**
28891867 AAATTTG
196 AAATTAC
* * * **
28891874 TATAAATAATAATTAATTATAAACAGTATGTTATAAAAACTAAGGTGATAATTAATAAGGTTATT
1 TATAAATAATAATTAATTATAAACAGTATGTAATAAAAACTAAAGTGATAACTAATAAAATTATT
*
28891939 AAGTGTAATCATATAAATAAAATTTATTATAAATTATAGTAAT-TGTTATGTATAAATT-AA-AT
66 AAGTGTAATCATATAAATAAAATCTATTATAAATTATAGTAATGT-TTATGTATAAATTAAACAT
*
28892001 --ATATATATATATAATGT-TTA-TATATATATATATATAT
130 ACATATATATATATAATATATTACTATAT-TATATATATAT
28892038 ATATATATAT
Statistics
Matches: 144, Mismatches: 15, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
196 4 0.03
197 13 0.09
198 14 0.10
199 19 0.13
200 4 0.03
201 4 0.03
202 86 0.60
ACGTcount: A:0.48, C:0.04, G:0.08, T:0.40
Consensus pattern (202 bp):
TATAAATAATAATTAATTATAAACAGTATGTAATAAAAACTAAAGTGATAACTAATAAAATTATT
AAGTGTAATCATATAAATAAAATCTATTATAAATTATAGTAATGTTTATGTATAAATTAAACATA
CATATATATATATAATATATTACTATATTATATATATATGAAACTAATGACACAACTTTAAATCA
AAATTAC
Found at i:28917332 original size:22 final size:22
Alignment explanation
Indices: 28917307--28917350 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
28917297 GTAAAGTAAA
28917307 ATATACAAGTACCTTCAACTTT
1 ATATACAAGTACCTTCAACTTT
28917329 ATATACAAGTACCTTCAACTTT
1 ATATACAAGTACCTTCAACTTT
28917351 TAATCATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.23, G:0.05, T:0.36
Consensus pattern (22 bp):
ATATACAAGTACCTTCAACTTT
Found at i:28921179 original size:34 final size:34
Alignment explanation
Indices: 28921141--28921205 Score: 130
Period size: 34 Copynumber: 1.9 Consensus size: 34
28921131 GAGTAAGGCC
28921141 TTTTTTCTTTCCTTTTTACAATTGATGGTAAGCA
1 TTTTTTCTTTCCTTTTTACAATTGATGGTAAGCA
28921175 TTTTTTCTTTCCTTTTTACAATTGATGGTAA
1 TTTTTTCTTTCCTTTTTACAATTGATGGTAA
28921206 AATTATCTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.20, C:0.14, G:0.11, T:0.55
Consensus pattern (34 bp):
TTTTTTCTTTCCTTTTTACAATTGATGGTAAGCA
Found at i:28925169 original size:24 final size:26
Alignment explanation
Indices: 28925125--28925178 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 26
28925115 TGATATTTTC
*
28925125 AATAATTTGCTCATCACGAA-TA-AT
1 AATAATTTGCTAATCACGAATTAGAT
*
28925149 AATAATTTG-TAATTCAGGAATTAGAT
1 AATAATTTGCTAA-TCACGAATTAGAT
28925175 AATA
1 AATA
28925179 TTCGTATAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
23 2 0.08
24 15 0.60
25 2 0.08
26 6 0.24
ACGTcount: A:0.44, C:0.09, G:0.11, T:0.35
Consensus pattern (26 bp):
AATAATTTGCTAATCACGAATTAGAT
Found at i:28932818 original size:20 final size:22
Alignment explanation
Indices: 28932787--28932826 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
28932777 ATCTTTCTTT
28932787 TCTTTGAGCAGATCT-GATTAC
1 TCTTTGAGCAGATCTCGATTAC
28932808 TCTTT-AGCAGATCTCGATT
1 TCTTTGAGCAGATCTCGATT
28932827 TTTACTGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.23, C:0.20, G:0.17, T:0.40
Consensus pattern (22 bp):
TCTTTGAGCAGATCTCGATTAC
Found at i:28934095 original size:18 final size:18
Alignment explanation
Indices: 28934068--28934109 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
28934058 TTTATTATTA
*
28934068 TTTTTCTTGTTTCATTTC
1 TTTTTCTTGTTTAATTTC
*
28934086 TTTTTGTTGTTTAATTTC
1 TTTTTCTTGTTTAATTTC
28934104 TCTTTT
1 T-TTTT
28934110 TTCAAAAGGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 17 0.81
19 4 0.19
ACGTcount: A:0.07, C:0.12, G:0.07, T:0.74
Consensus pattern (18 bp):
TTTTTCTTGTTTAATTTC
Found at i:28962302 original size:15 final size:16
Alignment explanation
Indices: 28962276--28962305 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
28962266 TTGGACACGG
28962276 GAATTAAAAACAAAAA
1 GAATTAAAAACAAAAA
28962292 GAATT-AAAACAAAA
1 GAATTAAAAACAAAA
28962306 TCCTATGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.73, C:0.07, G:0.07, T:0.13
Consensus pattern (16 bp):
GAATTAAAAACAAAAA
Found at i:28966125 original size:2 final size:2
Alignment explanation
Indices: 28966118--28966154 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
28966108 GAGAAAGTGC
*
28966118 AT AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
28966155 GAGCATGGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:28969040 original size:29 final size:28
Alignment explanation
Indices: 28969008--28969098 Score: 84
Period size: 27 Copynumber: 3.3 Consensus size: 28
28968998 TTTTTTTTAA
28969008 AAAATATATATAAATTATTTATAAAATTT
1 AAAATAT-TATAAATTATTTATAAAATTT
* *
28969037 AAAATATTA-ATATT-TTATATATAATTT
1 AAAATATTATAAATTATT-TATAAAATTT
* *
28969064 -AAATATTATTAA-TATTAATATAAA-TT
1 AAAATATTATAAATTATTTATA-AAATTT
28969090 AAAATATTA
1 AAAATATTA
28969099 AATATTAATA
Statistics
Matches: 51, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
26 16 0.31
27 26 0.51
28 2 0.04
29 7 0.14
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (28 bp):
AAAATATTATAAATTATTTATAAAATTT
Found at i:28969057 original size:27 final size:27
Alignment explanation
Indices: 28969027--28969109 Score: 93
Period size: 27 Copynumber: 3.1 Consensus size: 27
28969017 ATAAATTATT
*
28969027 TATAAAATTTAAAATATTAATATTTTA
1 TATAAAATTTAAAATATTAATATTTAA
*
28969054 TATATAATTTAAATATTATTAATA-TTAA
1 TATAAAATTTAAA-A-TATTAATATTTAA
28969082 TAT-AAA-TTAAAATATTAA-ATATTAA
1 TATAAAATTTAAAATATTAATAT-TTAA
28969107 TAT
1 TAT
28969110 TTTAAATTAT
Statistics
Matches: 49, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
23 1 0.02
24 6 0.12
25 8 0.16
26 5 0.10
27 14 0.29
28 7 0.14
29 8 0.16
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (27 bp):
TATAAAATTTAAAATATTAATATTTAA
Found at i:28969058 original size:15 final size:15
Alignment explanation
Indices: 28969040--28969157 Score: 75
Period size: 15 Copynumber: 7.9 Consensus size: 15
28969030 AAAATTTAAA
28969040 ATATTAATATTTTAT
1 ATATTAATATTTTAT
**
28969055 ATA-TAAT-TTAAAT
1 ATATTAATATTTTAT
*
28969068 ATTATTAATATTAATAT
1 A-TATTAATATT-TTAT
* * * *
28969085 AAATTAAAATATTAA
1 ATATTAATATTTTAT
*
28969100 ATATTAATATTTTAA
1 ATATTAATATTTTAT
28969115 AT-TATAATATTTTAT
1 ATAT-TAATATTTTAT
*
28969130 TTATTAA-ATTATTAAT
1 ATATTAATATT-TT-AT
28969146 ATATTAA-ATTTT
1 ATATTAATATTTT
28969158 TAATGAAAAA
Statistics
Matches: 81, Mismatches: 14, Indels: 16
0.73 0.13 0.14
Matches are distributed among these distances:
13 5 0.06
14 10 0.12
15 41 0.51
16 21 0.26
17 4 0.05
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
ATATTAATATTTTAT
Found at i:28969103 original size:60 final size:63
Alignment explanation
Indices: 28969029--28969148 Score: 160
Period size: 60 Copynumber: 2.0 Consensus size: 63
28969019 AAATTATTTA
*
28969029 TAAAATTTAAAATATTAATATTTTATA-TATAAT-TTAAATATTATT-AA-TATTAATATAAAT
1 TAAAATTTAAAATATTAATATTTTAAATTATAATATTAAAT-TTATTAAATTATTAATATAAAT
**
28969089 TAAAATATT-AAATATTAATATTTTAAATTATAATATTTTATTTATTAAATTATTAATATA
1 TAAAAT-TTAAAATATTAATATTTTAAATTATAATATTAAATTTATTAAATTATTAATATA
28969149 TTAAATTTTT
Statistics
Matches: 52, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
60 23 0.44
61 13 0.25
62 6 0.12
63 10 0.19
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (63 bp):
TAAAATTTAAAATATTAATATTTTAAATTATAATATTAAATTTATTAAATTATTAATATAAAT
Found at i:28969232 original size:37 final size:39
Alignment explanation
Indices: 28969184--28969276 Score: 102
Period size: 37 Copynumber: 2.4 Consensus size: 39
28969174 AAAAATTATT
* *
28969184 AATATTTTTAATTATAATA-A-T-ATTAAATTATATAAAA
1 AATATTATTAATTAAAATATAGTAATTAAATTATAT-AAA
*
28969221 AATATTATTAATTAAAATATTAGTAATTAAATTATATTAA
1 AATATTATTAATTAAAATA-TAGTAATTAAATTATATAAA
* *
28969261 AATATTAATATTTAAA
1 AATATTATTAATTAAA
28969277 TTATTAATTA
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
37 17 0.36
39 1 0.02
40 17 0.36
41 12 0.26
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (39 bp):
AATATTATTAATTAAAATATAGTAATTAAATTATATAAA
Found at i:28969237 original size:15 final size:15
Alignment explanation
Indices: 28969219--28969317 Score: 68
Period size: 15 Copynumber: 6.9 Consensus size: 15
28969209 AATTATATAA
28969219 AAAATATTATTAATT
1 AAAATATTATTAATT
*
28969234 AAAATATTAGTAATT
1 AAAATATTATTAATT
28969249 --AA-ATTA-T-ATT
1 AAAATATTATTAATT
* *
28969259 AAAATATTAATATTT
1 AAAATATTATTAATT
*
28969274 AAATTATTAATT-ATT
1 AAAATATT-ATTAATT
* *
28969289 AATATTTTAATTAATT
1 AAAATATT-ATTAATT
*
28969305 ATAA-ATTATTAAT
1 AAAATATTATTAAT
28969318 ATTTAAAAAT
Statistics
Matches: 66, Mismatches: 11, Indels: 15
0.72 0.12 0.16
Matches are distributed among these distances:
10 3 0.05
11 1 0.02
12 6 0.09
13 6 0.09
14 7 0.11
15 36 0.55
16 7 0.11
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (15 bp):
AAAATATTATTAATT
Found at i:28969264 original size:25 final size:25
Alignment explanation
Indices: 28969227--28969324 Score: 89
Period size: 25 Copynumber: 4.0 Consensus size: 25
28969217 AAAAAATATT
*
28969227 ATTA-ATTAAAATATTAGTAATTAA
1 ATTATATTAAAATATTAATAATTAA
*
28969251 ATTATATTAAAATATTAATATTTAA
1 ATTATATTAAAATATTAATAATTAA
* * *
28969276 A-T-TATT-AATTATTAATATTTTA
1 ATTATATTAAAATATTAATAATTAA
*
28969298 ATTA-ATTATAAATTATTAATATTTAA
1 ATTATATTA-AAA-TATTAATAATTAA
28969324 A
1 A
28969325 AATAAAATAA
Statistics
Matches: 62, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
22 15 0.24
23 8 0.13
24 5 0.08
25 21 0.34
26 13 0.21
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (25 bp):
ATTATATTAAAATATTAATAATTAA
Found at i:28969285 original size:37 final size:37
Alignment explanation
Indices: 28969086--28969286 Score: 104
Period size: 41 Copynumber: 5.1 Consensus size: 37
28969076 TATTAATATA
*
28969086 AATTAAA--ATATT-AAATATTAATATTTTAAATTATA
1 AATTAAATTATATTAAAATATTAATA-TTTAAATTATT
** * *
28969121 ATATTTTATT-TATTAAATTATTAATATATTAAATTTTT
1 A-ATTAAATTATATTAAAATATTAATAT-TTAAATTATT
* * * ** *
28969159 AATGAAAAATAAAAAAAAAATTATTAATATTTTTAATTATAAT
1 AAT--TAAATTATATTAAAA-TATTAATA-TTTAAATTAT--T
* * * *
28969202 AATATTAAATTATATAAAAAATATTATTAATTAAAATATTAGT
1 -A-ATTAAATTATAT-TAAAATATTAAT-ATT-TAA-ATTATT
28969245 AATTAAATTATATTAAAATATTAATATTTAAATTATT
1 AATTAAATTATATTAAAATATTAATATTTAAATTATT
28969282 AATTA
1 AATTA
28969287 TTAATATTTT
Statistics
Matches: 121, Mismatches: 27, Indels: 34
0.66 0.15 0.19
Matches are distributed among these distances:
35 1 0.01
36 4 0.03
37 17 0.14
38 21 0.17
39 5 0.04
40 14 0.12
41 27 0.22
42 2 0.02
43 16 0.13
44 8 0.07
45 6 0.05
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (37 bp):
AATTAAATTATATTAAAATATTAATATTTAAATTATT
Found at i:28969334 original size:26 final size:26
Alignment explanation
Indices: 28969249--28969335 Score: 67
Period size: 26 Copynumber: 3.5 Consensus size: 26
28969239 ATTAGTAATT
* * *
28969249 AAATTATATTAAAATATTAATATTT-
1 AAATAATAATAAATTATTAATATTTA
* *
28969274 AAAT--T-ATTAATTATTAATATTTT
1 AAATAATAATAAATTATTAATATTTA
* *
28969297 AATTAATTATAAATTATTAATATTTAA
1 AAATAATAATAAATTATTAATATTT-A
28969324 AAATAA-AATAAA
1 AAATAATAATAAA
28969336 AAATAATTAN
Statistics
Matches: 49, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
22 14 0.29
23 4 0.08
25 5 0.10
26 21 0.43
27 5 0.10
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (26 bp):
AAATAATAATAAATTATTAATATTTA
Found at i:28972634 original size:129 final size:129
Alignment explanation
Indices: 28972262--28972608 Score: 545
Period size: 129 Copynumber: 2.7 Consensus size: 129
28972252 CTCAAAGAAA
* *
28972262 TTTTAACTGTTGCTTGATTCAGGGAAAAGAAAGAATGCAATGTTATTCTTCAGAGCTGTAGAATA
1 TTTTAACTGATGCTTGATTCA-GGAATAGAAAGAATGCAATGTTATTCTTCAGAGCTGTAGAATA
28972327 TGGAACTGATTTCATTGGTCCATAAGATTACCTGATCTTTTAGTCTTTTAGGTGGGAGGATACAT
65 TGGAACTGATTTCATTGGTCCATAAGATTACCTGATCTTTTAGTCTTTTAGGTGGGAGGATACAT
* **
28972392 TTTTAACTGATGCTTTATTTGGGAATAGAAAGAATGCAATGTTATTCTT-ATGAGCTGTAGAATA
1 TTTTAACTGATGCTTGATTCAGGAATAGAAAGAATGCAATGTTATTCTTCA-GAGCTGTAGAATA
28972456 TGGAACTGATTTCATTGGTCCATAAGATTACCTGATCTTTTAGTCTTTTAGGTGGGAGGATACAT
65 TGGAACTGATTTCATTGGTCCATAAGATTACCTGATCTTTTAGTCTTTTAGGTGGGAGGATACAT
* * * **
28972521 TTTTAACTGATGCTTGATTCAGGAATGGAAAGAATGCATTGTTATTCTTCAGAGCTATA-AGCAT
1 TTTTAACTGATGCTTGATTCAGGAATAGAAAGAATGCAATGTTATTCTTCAGAGCTGTAGAATAT
* **
28972585 GGAACTGATCTCGGTGGTCCATAA
66 GGAACTGATTTCATTGGTCCATAA
28972609 CCAACTGTAC
Statistics
Matches: 199, Mismatches: 16, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
128 25 0.13
129 156 0.78
130 18 0.09
ACGTcount: A:0.29, C:0.12, G:0.22, T:0.36
Consensus pattern (129 bp):
TTTTAACTGATGCTTGATTCAGGAATAGAAAGAATGCAATGTTATTCTTCAGAGCTGTAGAATAT
GGAACTGATTTCATTGGTCCATAAGATTACCTGATCTTTTAGTCTTTTAGGTGGGAGGATACAT
Found at i:28982634 original size:20 final size:20
Alignment explanation
Indices: 28982611--28982649 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
28982601 TAAAAGATAT
*
28982611 ATATATATATATTACTTTTA
1 ATATAAATATATTACTTTTA
28982631 ATATAAATATATTACTTTT
1 ATATAAATATATTACTTTT
28982650 TATTTTGTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (20 bp):
ATATAAATATATTACTTTTA
Found at i:28982921 original size:23 final size:24
Alignment explanation
Indices: 28982888--28982934 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
28982878 CTTGTAATGT
28982888 CTTTAAATATATATACTTTATATA
1 CTTTAAATATATATACTTTATATA
*
28982912 CTTT-AATATATATATTTTATATA
1 CTTTAAATATATATACTTTATATA
28982935 TATTAGATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 18 0.82
24 4 0.18
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.53
Consensus pattern (24 bp):
CTTTAAATATATATACTTTATATA
Found at i:28989657 original size:11 final size:11
Alignment explanation
Indices: 28989641--28989702 Score: 52
Period size: 11 Copynumber: 5.3 Consensus size: 11
28989631 TGCAATTCTC
*
28989641 TATTTTTTTGT
1 TATTTTTTTAT
28989652 TATTTTTTTAT
1 TATTTTTTTAT
**
28989663 TATTTAATTAT
1 TATTTTTTTAT
28989674 TATTGTCATTTTAT
1 TATT-T--TTTTAT
*
28989688 TTTATTTTTTAT
1 TAT-TTTTTTAT
28989700 TAT
1 TAT
28989703 CATATTTTCT
Statistics
Matches: 40, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
11 23 0.57
12 9 0.22
14 7 0.17
15 1 0.03
ACGTcount: A:0.21, C:0.02, G:0.03, T:0.74
Consensus pattern (11 bp):
TATTTTTTTAT
Found at i:28989710 original size:20 final size:18
Alignment explanation
Indices: 28989681--28989739 Score: 57
Period size: 20 Copynumber: 3.1 Consensus size: 18
28989671 TATTATTGTC
28989681 ATTT-TATTTTATTTTTT
1 ATTTCTATTTTATTTTTT
* *
28989698 ATTATCATATTTTCTATTTT
1 ATT-TC-TATTTTATTTTTT
28989718 ATTTCTAATTATTATTTTTT
1 ATTTCT-ATT-TTATTTTTT
28989738 AT
1 AT
28989740 ACTTTACGTT
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
17 3 0.09
18 2 0.06
19 5 0.15
20 23 0.70
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (18 bp):
ATTTCTATTTTATTTTTT
Found at i:28989737 original size:27 final size:26
Alignment explanation
Indices: 28989657--28989737 Score: 81
Period size: 27 Copynumber: 2.9 Consensus size: 26
28989647 TTTGTTATTT
28989657 TTTTATTATTTAATTATTATTGTCATTTTA
1 TTTTATT-TTTAATTATTATT-T--TTTTA
* * *
28989687 TTTTATTTTTTATTATCATATTTTCTA
1 TTTTATTTTTAATTATTAT-TTTTTTA
*
28989714 TTTTATTTCTAATTATTATTTTTT
1 TTTTATTTTTAATTATTATTTTTT
28989738 ATACTTTACG
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
26 4 0.09
27 20 0.47
29 11 0.26
30 8 0.19
ACGTcount: A:0.23, C:0.05, G:0.01, T:0.70
Consensus pattern (26 bp):
TTTTATTTTTAATTATTATTTTTTTA
Found at i:28989745 original size:27 final size:27
Alignment explanation
Indices: 28989681--28989745 Score: 62
Period size: 27 Copynumber: 2.5 Consensus size: 27
28989671 TATTATTGTC
* *
28989681 ATTTTAT--TTTATTTTTTATTATCAT
1 ATTTTATACTTTATTTCTAATTATCAT
* * *
28989706 ATTTTCTATTTTATTTCTAATTATTAT
1 ATTTTATACTTTATTTCTAATTATCAT
*
28989733 TTTTTATACTTTA
1 ATTTTATACTTTA
28989746 CGTTTTTTGT
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
25 6 0.19
27 25 0.81
ACGTcount: A:0.25, C:0.06, G:0.00, T:0.69
Consensus pattern (27 bp):
ATTTTATACTTTATTTCTAATTATCAT
Found at i:28989951 original size:15 final size:15
Alignment explanation
Indices: 28989933--28989994 Score: 54
Period size: 16 Copynumber: 3.9 Consensus size: 15
28989923 TATATTCGAA
28989933 TTATTATTATTTTTT
1 TTATTATTATTTTTT
* *
28989948 TTATCATCAATTTTTT
1 TTATTAT-TATTTTTT
*
28989964 ATCTATTATTA-TTTAT
1 -T-TATTATTATTTTTT
28989980 TTATTTATTATTTTT
1 TTA-TTATTATTTTT
28989995 ATTGAGTAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 9
0.71 0.12 0.18
Matches are distributed among these distances:
14 2 0.06
15 13 0.36
16 14 0.39
17 2 0.06
18 5 0.14
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (15 bp):
TTATTATTATTTTTT
Found at i:28989981 original size:21 final size:21
Alignment explanation
Indices: 28989957--28989997 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
28989947 TTTATCATCA
28989957 ATTT-TTTATCTATTATTATTT
1 ATTTATTTAT-TATTATTATTT
*
28989978 ATTTATTTATTATTTTTATT
1 ATTTATTTATTATTATTATT
28989998 GAGTAATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.73
Consensus pattern (21 bp):
ATTTATTTATTATTATTATTT
Found at i:28989982 original size:18 final size:18
Alignment explanation
Indices: 28989957--28989997 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
28989947 TTTATCATCA
28989957 ATTT-TTTATCTATTATT
1 ATTTATTTATCTATTATT
*
28989974 ATTTATTTATTTATTATT
1 ATTTATTTATCTATTATT
28989992 -TTTATT
1 ATTTATT
28989998 GAGTAATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 10 0.45
18 12 0.55
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.73
Consensus pattern (18 bp):
ATTTATTTATCTATTATT
Found at i:28991893 original size:1 final size:1
Alignment explanation
Indices: 28991887--28991994 Score: 63
Period size: 1 Copynumber: 108.0 Consensus size: 1
28991877 TTACCAAAGC
* * * * * * * * * *
28991887 TTTTTTTTTTGTTGTTTTTTTTTTGTTTTGTTTTGTTTGTTTTTTGTTTGTTTTGTTTTTTTTAT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * * * * *
28991952 CTTTTTGTTTTTTATTGTTGTTTTTTTTGTTTGTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
28991995 AAATGAGACT
Statistics
Matches: 73, Mismatches: 34, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
1 73 1.00
ACGTcount: A:0.02, C:0.01, G:0.13, T:0.84
Consensus pattern (1 bp):
T
Found at i:28991907 original size:15 final size:14
Alignment explanation
Indices: 28991887--28991994 Score: 110
Period size: 14 Copynumber: 7.5 Consensus size: 14
28991877 TTACCAAAGC
*
28991887 TTTTTTTTTTGTTG
1 TTTTTTTTTTGTTT
28991901 TTTTTTTTTTGTTT
1 TTTTTTTTTTGTTT
* *
28991915 TGTTTTGTTTGTTT
1 TTTTTTTTTTGTTT
28991929 TTTGTTTGTTTTGTTT
1 TTT-TTT-TTTTGTTT
* *
28991945 TTTTTATCTT-TTT
1 TTTTTTTTTTGTTT
* *
28991958 GTTTTTTATTGTTGT
1 TTTTTTTTTTGTT-T
28991973 TTTTTTTGTTTGTTT
1 TTTTTTT-TTTGTTT
28991988 TTTTTTT
1 TTTTTTT
28991995 AAATGAGACT
Statistics
Matches: 77, Mismatches: 12, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
13 10 0.13
14 32 0.42
15 20 0.26
16 15 0.19
ACGTcount: A:0.02, C:0.01, G:0.13, T:0.84
Consensus pattern (14 bp):
TTTTTTTTTTGTTT
Found at i:28991908 original size:16 final size:16
Alignment explanation
Indices: 28991887--28991994 Score: 96
Period size: 17 Copynumber: 6.4 Consensus size: 16
28991877 TTACCAAAGC
28991887 TTTTTTTTTTGTTGTT
1 TTTTTTTTTTGTTGTT
28991903 TTTTTTTTGTT-TTGTTT
1 TTTTTTTT-TTGTTG-TT
28991920 TGTTTGTTTTTTGTTTGTT
1 T-TTT-TTTTTTG-TTGTT
*
28991939 TTGTTTTTTTTATCT-TT
1 TT-TTTTTTTTGT-TGTT
28991956 TTGTTTTTTATTGTTGTT
1 TT-TTTTTT-TTGTTGTT
*
28991974 TTTTTTGTTTGTT-TT
1 TTTTTTTTTTGTTGTT
28991989 TTTTTT
1 TTTTTT
28991995 AAATGAGACT
Statistics
Matches: 79, Mismatches: 3, Indels: 21
0.77 0.03 0.20
Matches are distributed among these distances:
15 8 0.10
16 16 0.20
17 23 0.29
18 20 0.25
19 9 0.11
20 3 0.04
ACGTcount: A:0.02, C:0.01, G:0.13, T:0.84
Consensus pattern (16 bp):
TTTTTTTTTTGTTGTT
Found at i:28992070 original size:38 final size:38
Alignment explanation
Indices: 28991995--28992489 Score: 488
Period size: 38 Copynumber: 13.1 Consensus size: 38
28991985 TTTTTTTTTT
* * *
28991995 AAATGAGACTCCTCAAAGTTGAGGCGACAAAAC-TTTAA
1 AAATGA-ACTCCTCAAAGCTGAGGCAACGAAACTTTTAA
** * *
28992033 AAATGAACTCCTCAAAATTGAGACTACGAAACTTTTAAA
1 AAATGAACTCCTCAAAGCTGAGGCAACGAAACTTTT-AA
* *
28992072 AAATGAAACT-TTCCAAAGCTGAGGCAACGAAACTTCTAA
1 AAATG-AACTCCT-CAAAGCTGAGGCAACGAAACTTTTAA
*
28992111 AAATGAATTCCTCAAAGCTGAGGCAACG-AACTTTT-A
1 AAATGAACTCCTCAAAGCTGAGGCAACGAAACTTTTAA
*
28992147 AAATGAACTCCTCAAAGCTGAGGCAACGAAACTTCTAA
1 AAATGAACTCCTCAAAGCTGAGGCAACGAAACTTTTAA
* * * *
28992185 AGATGAACTCTTCAAAGCTGAGGCAATGATACTTTTAA
1 AAATGAACTCCTCAAAGCTGAGGCAACGAAACTTTTAA
* ** *
28992223 AAATGAACTCCTCAAAACTGAGGCAACGGGACTTCTAA
1 AAATGAACTCCTCAAAGCTGAGGCAACGAAACTTTTAA
* * * *
28992261 AAATGAACTCTTCAAAGCTGAGACAACAAAACTTCT-A
1 AAATGAACTCCTCAAAGCTGAGGCAACGAAACTTTTAA
* * *
28992298 AAATGAACTCCTCAAAGCTTAGGCAACGAGACCTTTAA
1 AAATGAACTCCTCAAAGCTGAGGCAACGAAACTTTTAA
* * **
28992336 AAATGAACTTCTCAAAGCTGAGGCAATGTGA-TTTTAA
1 AAATGAACTCCTCAAAGCTGAGGCAACGAAACTTTTAA
* * **
28992373 AAATGTACTTCTCAAAGCTGAGGCAACGTGAC-TTTAA
1 AAATGAACTCCTCAAAGCTGAGGCAACGAAACTTTTAA
** ***
28992410 AAATGTGGCTCCTCAAAGCTGAGGCAACTTGAC-TTTAA
1 AAATG-AACTCCTCAAAGCTGAGGCAACGAAACTTTTAA
**
28992448 AAATGTGGCTCCTCAAAGCTGAGGCAAC-ATAAC-TTTAA
1 AAATG-AACTCCTCAAAGCTGAGGCAACGA-AACTTTTAA
28992486 AAAT
1 AAAT
28992490 CTTGAAACTA
Statistics
Matches: 393, Mismatches: 53, Indels: 22
0.84 0.11 0.05
Matches are distributed among these distances:
36 28 0.07
37 108 0.27
38 218 0.55
39 16 0.04
40 23 0.06
ACGTcount: A:0.40, C:0.20, G:0.17, T:0.24
Consensus pattern (38 bp):
AAATGAACTCCTCAAAGCTGAGGCAACGAAACTTTTAA
Found at i:28992294 original size:151 final size:148
Alignment explanation
Indices: 28991990--28992489 Score: 542
Period size: 150 Copynumber: 3.3 Consensus size: 148
28991980 GTTTGTTTTT
* * * * * **
28991990 TTTTTAAATGAGACTCCTCAAAGTTGAGGCGACAAAACTTTAAAAATGAACTCCTCAAAATTGAG
1 TTTTAAAATGA-ACTCCTCAAAGCTGAGGCAACGAAACTTTAAAAATGAACTCTTCAAAGCTGAG
* * * * * * *
28992055 ACTACGAAACTTTTAAAAAATGAAACTTTCCAAAGCTGAGGCAACGAAACTTCTAAAAATGAATT
65 GCAATGATACTTTT-AAAAATG-AACTCT-CAAAGCTGAGGCAACGAGACTTCTAAAAATGAACT
*
28992120 CCTCAAAGCTGAGGCAACGAAC
127 CCTCAAAGCTGAGGCAACAAAC
*
28992142 TTTTAAAATGAACTCCTCAAAGCTGAGGCAACGAAACTTCTAAAGATGAACTCTTCAAAGCTGAG
1 TTTTAAAATGAACTCCTCAAAGCTGAGGCAACGAAACTT-TAAAAATGAACTCTTCAAAGCTGAG
* * *
28992207 GCAATGATACTTTTAAAAATGAACTCCTCAAAACTGAGGCAACGGGACTTCTAAAAATGAACTCT
65 GCAATGATACTTTTAAAAATGAACT-CTCAAAGCTGAGGCAACGAGACTTCTAAAAATGAACTCC
*
28992272 TCAAAGCTGAGACAACAAAAC
129 TCAAAGCTGAGGCAAC-AAAC
* * *
28992293 TTCTAAAATGAACTCCTCAAAGCTTAGGCAACGAGACCTTTAAAAATGAACT-TCTCAAAGCTGA
1 TTTTAAAATGAACTCCTCAAAGCTGAGGCAACGA-AACTTTAAAAATGAACTCT-TCAAAGCTGA
* * **
28992357 GGCAATG-TGA-TTTTAAAAATGTACTTCTCAAAGCTGAGGCAACGTGACTT-TAAAAATGTGGC
64 GGCAATGAT-ACTTTTAAAAATGAAC-TCTCAAAGCTGAGGCAACGAGACTTCTAAAAATG-AAC
**
28992419 TCCTCAAAGCTGAGGCAACTTGAC
126 TCCTCAAAGCTGAGGCAAC-AAAC
* **
28992443 TTTAAAAATGTGGCTCCTCAAAGCTGAGGCAAC-ATAACTTTAAAAAT
1 TTTTAAAATG-AACTCCTCAAAGCTGAGGCAACGA-AACTTTAAAAAT
28992490 CTTGAAACTA
Statistics
Matches: 298, Mismatches: 41, Indels: 20
0.83 0.11 0.06
Matches are distributed among these distances:
149 8 0.03
150 128 0.43
151 117 0.39
152 45 0.15
ACGTcount: A:0.40, C:0.20, G:0.16, T:0.24
Consensus pattern (148 bp):
TTTTAAAATGAACTCCTCAAAGCTGAGGCAACGAAACTTTAAAAATGAACTCTTCAAAGCTGAGG
CAATGATACTTTTAAAAATGAACTCTCAAAGCTGAGGCAACGAGACTTCTAAAAATGAACTCCTC
AAAGCTGAGGCAACAAAC
Found at i:28992336 original size:113 final size:114
Alignment explanation
Indices: 28991995--28992489 Score: 493
Period size: 113 Copynumber: 4.4 Consensus size: 114
28991985 TTTTTTTTTT
* * *** ** *
28991995 AAATGAGACTCCTCAAAGTTGAGGCGACAAAACTTTAAAAATGAACTCCTCAAAATTGAGACTAC
1 AAATGA-ACTCCTCAAAGCTGAGGCAACGGGACTTTAAAAATGAACTCCTCAAAGCTGAGACAAC
* * *
28992060 GAAACTTTTAAAAAATGAAACT-TTCCAAAGCTGAGGCAACGA-AACTTCTAA
65 GAAACTTCT-AAAAATGAAACTCCT-CAAAGCTGAGGCAACGAGACCTT-TAA
* * * *
28992111 AAATGAATTCCTCAAAGCTGAGGCAAC-GAACTTTTAAAATGAACTCCTCAAAGCTGAGGCAACG
1 AAATGAACTCCTCAAAGCTGAGGCAACGGGACTTTAAAAATGAACTCCTCAAAGCTGAGACAACG
* * * * *
28992175 AAACTTCTAAAGATG-AACTCTTCAAAGCTGAGGCAATGATACTTTTAA
66 AAACTTCTAAAAATGAAACTCCTCAAAGCTGAGGCAACGAGACCTTTAA
* *
28992223 AAATGAACTCCTCAAAACTGAGGCAACGGGACTTCTAAAAATGAACTCTTCAAAGCTGAGACAAC
1 AAATGAACTCCTCAAAGCTGAGGCAACGGGACTT-TAAAAATGAACTCCTCAAAGCTGAGACAAC
* *
28992288 AAAACTTCT-AAAATG-AACTCCTCAAAGCTTAGGCAACGAGACCTTTAA
65 GAAACTTCTAAAAATGAAACTCCTCAAAGCTGAGGCAACGAGACCTTTAA
* * * * * * *
28992336 AAATGAACTTCTCAAAGCTGAGGCAATGTGATTTTAAAAATGTACTTCTCAAAGCTGAGGCAACG
1 AAATGAACTCCTCAAAGCTGAGGCAACGGGACTTTAAAAATGAACTCCTCAAAGCTGAGACAACG
** *** **
28992401 TGACTT-TAAAAATGTGGCTCCTCAAAGCTGAGGCAACTTGA-CTTTAA
66 AAACTTCTAAAAATGAAACTCCTCAAAGCTGAGGCAACGAGACCTTTAA
** ***
28992448 AAATGTGGCTCCTCAAAGCTGAGGCAACATAACTTTAAAAAT
1 AAATG-AACTCCTCAAAGCTGAGGCAACGGGACTTTAAAAAT
28992490 CTTGAAACTA
Statistics
Matches: 321, Mismatches: 51, Indels: 17
0.83 0.13 0.04
Matches are distributed among these distances:
111 1 0.00
112 95 0.30
113 128 0.40
114 73 0.23
115 18 0.06
116 6 0.02
ACGTcount: A:0.40, C:0.20, G:0.17, T:0.24
Consensus pattern (114 bp):
AAATGAACTCCTCAAAGCTGAGGCAACGGGACTTTAAAAATGAACTCCTCAAAGCTGAGACAACG
AAACTTCTAAAAATGAAACTCCTCAAAGCTGAGGCAACGAGACCTTTAA
Found at i:28993809 original size:79 final size:79
Alignment explanation
Indices: 28993666--28993817 Score: 214
Period size: 79 Copynumber: 1.9 Consensus size: 79
28993656 ATGAATTCCC
* * * * *
28993666 ATCTTTGCTCTAGACTGCCCTTTTAGGTTTTCACCCTAGAGCTTCATCTTTTTCACTCACTTTTT
1 ATCTTCGCTATAGACTGCCCTTTCAGGTTTTCACCCTAGAGCTTCATATTTCTCACTCACTTTTT
*
28993731 TTTTTTTCATCTTT
66 TCTTTTTCATCTTT
* ***
28993745 ATCTTCGCTATAGACTGCCCTTTCGGGTTTTCACCCTAGAGCTTCATATTTCTCACTTGTTTTTT
1 ATCTTCGCTATAGACTGCCCTTTCAGGTTTTCACCCTAGAGCTTCATATTTCTCACTCACTTTTT
28993810 TCTTTTTC
66 TCTTTTTC
28993818 TTTTTTTTTT
Statistics
Matches: 63, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
79 63 1.00
ACGTcount: A:0.14, C:0.26, G:0.11, T:0.50
Consensus pattern (79 bp):
ATCTTCGCTATAGACTGCCCTTTCAGGTTTTCACCCTAGAGCTTCATATTTCTCACTCACTTTTT
TCTTTTTCATCTTT
Found at i:28994250 original size:19 final size:20
Alignment explanation
Indices: 28994199--28994251 Score: 65
Period size: 18 Copynumber: 2.7 Consensus size: 20
28994189 CCTTTCTTTT
*
28994199 TTTTTTCAATTTTCATTTTCA
1 TTTTTTCAATCTTCA-TTTCA
*
28994220 TTTTTTC-TTCTTCA-TTCA
1 TTTTTTCAATCTTCATTTCA
28994238 TTTTTTCAATCTTC
1 TTTTTTCAATCTTC
28994252 CTGTTGATGG
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
18 11 0.39
19 5 0.18
20 5 0.18
21 7 0.25
ACGTcount: A:0.15, C:0.19, G:0.00, T:0.66
Consensus pattern (20 bp):
TTTTTTCAATCTTCATTTCA
Found at i:28995034 original size:23 final size:25
Alignment explanation
Indices: 28994994--28995040 Score: 80
Period size: 23 Copynumber: 2.0 Consensus size: 25
28994984 TAGACACCTC
28994994 TAAAATAAATAATAATAATAAAATA
1 TAAAATAAATAATAATAATAAAATA
28995019 TAAAAT-AA-AATAATAATAAAAT
1 TAAAATAAATAATAATAATAAAAT
28995041 TTTTTTAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 14 0.64
24 2 0.09
25 6 0.27
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (25 bp):
TAAAATAAATAATAATAATAAAATA
Found at i:28995036 original size:11 final size:11
Alignment explanation
Indices: 28995004--28995040 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
28994994 TAAAATAAAT
28995004 AATAATAATAA
1 AATAATAATAA
*
28995015 AATATAAAATAA
1 AATA-ATAATAA
28995027 AATAATAATAA
1 AATAATAATAA
28995038 AAT
1 AAT
28995041 TTTTTTAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
11 13 0.57
12 10 0.43
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (11 bp):
AATAATAATAA
Found at i:28995530 original size:14 final size:14
Alignment explanation
Indices: 28995513--28995552 Score: 71
Period size: 14 Copynumber: 2.8 Consensus size: 14
28995503 GGAGAAGGAG
28995513 AAAGAAAAGAAGAA
1 AAAGAAAAGAAGAA
28995527 AAAGAAAAGAAGAA
1 AAAGAAAAGAAGAA
28995541 AAAGAGAAAGAA
1 AAAGA-AAAGAA
28995553 AGAAGGGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 19 0.76
15 6 0.24
ACGTcount: A:0.78, C:0.00, G:0.23, T:0.00
Consensus pattern (14 bp):
AAAGAAAAGAAGAA
Found at i:28995541 original size:22 final size:19
Alignment explanation
Indices: 28995511--28995557 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
28995501 AGGGAGAAGG
*
28995511 AGAAAGAA-AAGAAGAAAA
1 AGAAAGAAGAAAAAGAAAA
*
28995529 AGAAAAGAAGAAAAAGAGAA
1 AG-AAAGAAGAAAAAGAAAA
28995549 AGAAAGAAG
1 AGAAAGAAG
28995558 GGGAAAGAGG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 2 0.08
19 13 0.52
20 10 0.40
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (19 bp):
AGAAAGAAGAAAAAGAAAA
Found at i:28996067 original size:38 final size:36
Alignment explanation
Indices: 28996024--28996118 Score: 91
Period size: 38 Copynumber: 2.5 Consensus size: 36
28996014 TATAAAAATT
* *
28996024 ATAAAAAATAAAAATAAATTATGAAGAAGAATAAAGAA
1 ATAAAAAATAAAAATAAATAAT-AACAAGAA-AAAGAA
* * *
28996062 ATAAAAAAGAAAAAACATAATAATAACAAGAAATAGAA
1 ATAAAAAA-TAAAAATA-AATAATAACAAGAAAAAGAA
*
28996100 ATAATAAATAAATAATAAA
1 ATAAAAAATAAA-AATAAA
28996119 ATATACATTT
Statistics
Matches: 46, Mismatches: 8, Indels: 7
0.75 0.13 0.11
Matches are distributed among these distances:
37 5 0.11
38 23 0.50
39 13 0.28
40 5 0.11
ACGTcount: A:0.73, C:0.02, G:0.07, T:0.18
Consensus pattern (36 bp):
ATAAAAAATAAAAATAAATAATAACAAGAAAAAGAA
Found at i:28996299 original size:7 final size:7
Alignment explanation
Indices: 28996289--28996321 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
28996279 ATATAAAATG
28996289 AAATAAT
1 AAATAAT
28996296 AAATAA-
1 AAATAAT
28996302 AAATAAT
1 AAATAAT
28996309 AAATAAT
1 AAATAAT
28996316 AAATAA
1 AAATAA
28996322 ATTAAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 6 0.24
7 19 0.76
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (7 bp):
AAATAAT
Found at i:28996305 original size:13 final size:14
Alignment explanation
Indices: 28996289--28996321 Score: 59
Period size: 13 Copynumber: 2.4 Consensus size: 14
28996279 ATATAAAATG
28996289 AAATAATAAATAA-
1 AAATAATAAATAAT
28996302 AAATAATAAATAAT
1 AAATAATAAATAAT
28996316 AAATAA
1 AAATAA
28996322 ATTAAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (14 bp):
AAATAATAAATAAT
Found at i:29008346 original size:62 final size:61
Alignment explanation
Indices: 29008263--29008866 Score: 721
Period size: 62 Copynumber: 9.9 Consensus size: 61
29008253 CATTTATGAA
* * * * *
29008263 TTAAATCGAACCTGTTTTGAGATAGGTCTAACCTAAATTAAGTTTAAAAATTTCAATTTTGT
1 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTTTAGAAATTTCAATTTT-T
* * * *
29008325 TTAAATCGAACCCGCTGTGAGATAGGTCGAACCTAGATTAAGTCTAGAAATTTC-A-TTTT
1 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTTTAGAAATTTCAATTTTT
* * * * *
29008384 TTAAATCGAACTTATTGTGAGATAGGTCGAGCCTAGATCAAGTCTA-AGAATTTTAA-TTTT
1 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTTTAGA-AATTTCAATTTTT
* * * *
29008444 TTAAATCGAACCTGTTTGTGAGATGGGTCGAGCCTA-AGTCAA-TTCTAGGAATTTTAATTTTT
1 TTAAATCGAACCTG-TTGTGAGATAGGTCGAGCCTAGA-TTAAGTT-TAGAAATTTCAATTTTT
*
29008506 TTAAAATCGAACCTGTTTTGTTCTGAGATAGGTCGAGCCTAAATTAAGTTTA-AGAATTTCAATT
1 TT-AAATCGAACCTG--TTG---TGAGATAGGTCGAGCCTAGATTAAGTTTAGA-AATTTCAATT
29008570 TTGT
59 TT-T
*
29008574 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTTTAGGAATTTCAATTTTGT
1 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTTTAGAAATTTCAATTTT-T
29008636 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTTTAGAAATTTCAA---TT
1 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTTTAGAAATTTCAATTTTT
* * * * *
29008694 TTAAATTGAACCTGTTGTGAAATAGGTCAAGCCTAAATTAAGTTTAGAAATTTTAATTTTGT
1 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTTTAGAAATTTCAATTTT-T
* *
29008756 TTAAATTGAACCTGTTGTGAGATAAGTCGAGCCTAGATTAAGTTTAGAAATTTCAA---TT
1 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTTTAGAAATTTCAATTTTT
* *
29008814 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTT
1 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTTTAGAAATTT
29008867 TAATCGAATT
Statistics
Matches: 481, Mismatches: 40, Indels: 46
0.85 0.07 0.08
Matches are distributed among these distances:
58 103 0.21
59 48 0.10
60 22 0.05
61 36 0.07
62 202 0.42
63 12 0.02
64 4 0.01
65 3 0.01
67 45 0.09
68 6 0.01
ACGTcount: A:0.32, C:0.12, G:0.19, T:0.37
Consensus pattern (61 bp):
TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTTTAGAAATTTCAATTTTT
Found at i:29008729 original size:249 final size:245
Alignment explanation
Indices: 29008263--29008866 Score: 804
Period size: 249 Copynumber: 2.5 Consensus size: 245
29008253 CATTTATGAA
* * *
29008263 TTAAATCGAACCTG-T-TTTGAGATAGGTCTAACCTAAATTAAGTTTAAAAATTTCAATTTTGTT
1 TTAAATCGAACCTGTTGTTTGAGATAGGTCGAGCCTAAATTAAGTTTAAGAATTTCAATTTTGTT
* * * *
29008326 TAAATCGAACCCGCTGTGAGATAGGTCGAACCTAGATTAAGTCTAGAAATTTCATTTTTTAAATC
66 TAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTCATTTTTTAAATC
* *
29008391 GAACTTATTGTGAGATAGGTCGAGCCTAGATCAAGTCTAAGAATTTTAATTTTTTAAATCGAACC
131 GAACCTATTGTGAGATAGGTCGAGCCTAGATCAAGTCTAAGAATTTCAA-TTTTTAAATCGAACC
* * * * *
29008456 TGTTTGTGAGATGGGTCGAGCCTAAGTCAA-TTCTAGGAATTTTAATTTT-T
195 TGTTTGTGAAATAGGTCAAGCCTAAATCAAGTT-TAGAAATTTTAATTTTGT
29008506 TTAAAATCGAACCTGTTTTGTTCTGAGATAGGTCGAGCCTAAATTAAGTTTAAGAATTTCAATTT
1 TT-AAATCGAACCTG--TTGTT-TGAGATAGGTCGAGCCTAAATTAAGTTTAAGAATTTCAATTT
*
29008571 TGTTTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTTTAGGAATTTCAATTTTGT
62 TGTTTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTC-A-TTT-T
* * *
29008636 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGT-TTAGAAATTTCAA-TTTTAAA
124 TTAAATCGAACCTATTGTGAGATAGGTCGAGCCTAGATCAAGTCTAAG-AATTTCAATTTTTAAA
* *
29008699 TTGAACCTG-TTGTGAAATAGGTCAAGCCTAAATTAAGTTTAGAAATTTTAATTTTGT
188 TCGAACCTGTTTGTGAAATAGGTCAAGCCTAAATCAAGTTTAGAAATTTTAATTTTGT
* * *
29008756 TTAAATTGAACCTGTTG--TGAGATAAGTCGAGCCTAGATTAAGTTT-AGAAATTTCAA---T-T
1 TTAAATCGAACCTGTTGTTTGAGATAGGTCGAGCCTAAATTAAGTTTAAG-AATTTCAATTTTGT
29008814 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTT
65 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTT
29008867 TAATCGAATT
Statistics
Matches: 324, Mismatches: 24, Indels: 29
0.86 0.06 0.08
Matches are distributed among these distances:
240 53 0.16
241 1 0.00
243 4 0.01
244 46 0.14
247 4 0.01
248 2 0.01
249 139 0.43
250 21 0.06
251 6 0.02
252 48 0.15
ACGTcount: A:0.32, C:0.12, G:0.19, T:0.37
Consensus pattern (245 bp):
TTAAATCGAACCTGTTGTTTGAGATAGGTCGAGCCTAAATTAAGTTTAAGAATTTCAATTTTGTT
TAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTCATTTTTTAAATC
GAACCTATTGTGAGATAGGTCGAGCCTAGATCAAGTCTAAGAATTTCAATTTTTAAATCGAACCT
GTTTGTGAAATAGGTCAAGCCTAAATCAAGTTTAGAAATTTTAATTTTGT
Found at i:29008759 original size:182 final size:181
Alignment explanation
Indices: 29008263--29008964 Score: 713
Period size: 182 Copynumber: 3.9 Consensus size: 181
29008253 CATTTATGAA
* * * * *
29008263 TTAAATCGAACCTGTTTTGAGATAGGTCTAACCTAAATTAAGTTTAAAAATTTCAATTTTGTTTA
1 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTTTAGAAATTTCAA--TT-TTTA
* * * * *
29008328 AATCGAACCCGCTGTGAGATAGGTCGAA-CCTAGATTAAGTCTAGAAA-TTTCA-TTT-TTTAAA
63 AATCGAACCTGTTGTGAAATAGGTC-AAGCCTAAATTAAGTCTAGAAATTTTAATTTTGTTTAAA
* * * * * *
29008389 TCGAACTTATTGTGAGATAGGTCGAGCCTAGATCAAGTCTAAGAATTTTAATTTT
127 TCGAACCTATTGTGAGATAAGTCGAGCCTAGATTAAGTTTAGGAATTTCAATTTT
* * * *
29008444 TTAAATCGAACCTGTTTGTGAGATGGGTCGAGCCTA-AGTCAA-TTCTAGGAATTTTAATTTTTT
1 TTAAATCGAACCTG-TTGTGAGATAGGTCGAGCCTAGA-TTAAGTT-TAGAAATTTCAA--TTTT
* * * *
29008507 TAAAATCGAACCTGTTTTGTTCTGAGATAGGTCGAGCCTAAATTAAGTTTA-AGAATTTCAATTT
61 T-AAATCGAACCTG--TTG---TGAAATAGGTCAAGCCTAAATTAAGTCTAGA-AATTTTAATTT
* *
29008571 TGTTTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTTTAGGAATTTCAATTTTGT
119 TGTTTAAATCGAACCTATTGTGAGATAAGTCGAGCCTAGATTAAGTTTAGGAATTTCAA-TTT-T
29008636 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTTTAGAAATTTCAA-TTTTAAAT
1 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTTTAGAAATTTCAATTTTTAAAT
* * *
29008700 TGAACCTGTTGTGAAATAGGTCAAGCCTAAATTAAGTTTAGAAATTTTAATTTTGTTTAAATTGA
66 CGAACCTGTTGTGAAATAGGTCAAGCCTAAATTAAGTCTAGAAATTTTAATTTTGTTTAAATCGA
* *
29008765 ACCTGTTGTGAGATAAGTCGAGCCTAGATTAAGTTTAGAAATTTCAA--TT
131 ACCTATTGTGAGATAAGTCGAGCCTAGATTAAGTTTAGGAATTTCAATTTT
* *
29008814 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAG------GAA-TTTT-AAT
1 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTTTAGAAATTTCAATTTTTAAAT
** * * * * *
29008871 CGAATTTGTTCT-AATATGGGTCAAGCCTAGATCAAGTCTAGAAATTTTAATTTTTTTTAAATCG
66 CGAACCTGTTGTGAA-ATAGGTCAAGCCTAAATTAAGTCTAGAAATTTTAATTTTGTTTAAATCG
* * *
29008935 AACTTATTTTGAGATAAGTTGAGCCTAGAT
130 AACCTATTGTGAGATAAGTCGAGCCTAGAT
29008965 CGAATTGATT
Statistics
Matches: 453, Mismatches: 48, Indels: 50
0.82 0.09 0.09
Matches are distributed among these distances:
170 2 0.00
171 80 0.18
172 6 0.01
178 47 0.10
179 1 0.00
181 20 0.04
182 137 0.30
183 1 0.00
184 2 0.00
185 3 0.01
186 2 0.00
187 37 0.08
188 7 0.02
189 3 0.01
190 51 0.11
191 36 0.08
192 18 0.04
ACGTcount: A:0.32, C:0.12, G:0.19, T:0.37
Consensus pattern (181 bp):
TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTTTAGAAATTTCAATTTTTAAAT
CGAACCTGTTGTGAAATAGGTCAAGCCTAAATTAAGTCTAGAAATTTTAATTTTGTTTAAATCGA
ACCTATTGTGAGATAAGTCGAGCCTAGATTAAGTTTAGGAATTTCAATTTT
Found at i:29008867 original size:120 final size:119
Alignment explanation
Indices: 29008263--29008870 Score: 731
Period size: 120 Copynumber: 5.0 Consensus size: 119
29008253 CATTTATGAA
* * * *
29008263 TTAAATCGAACCTGTTTTGAGATAGGTCTAACCTAAATTAAGTTTAAAAATTTCAATTTTGTTTA
1 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTTT-AAAATTTCAA--TT-TTTA
* * * * *
29008328 AATCGAACCCGCTGTGAGATAGGTCGAACCTAGATTAAGTCTA-GAAATTTCA-TTTT
62 AATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTTAATTTTT
* * * * *
29008384 TTAAATCGAACTTATTGTGAGATAGGTCGAGCCTAGATCAAGTCTAAGAATTTTAATTTTTTAAA
1 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTTTAA-AATTTCAA-TTTTTAAA
* * *
29008449 TCGAACCTGTTTGTGAGATGGGTCGAGCCTA-AGTCAATTCTAGGAATTTTAATTTTT
64 TCGAACCTG-TTGTGAGATAGGTCGAGCCTAGA-TTAAGTCTAGGAATTTTAATTTTT
*
29008506 TTAAAATCGAACCTGTTTTGTTCTGAGATAGGTCGAGCCTAAATTAAGTTTAAGAATTTCAATTT
1 TT-AAATCGAACCTG--TTG---TGAGATAGGTCGAGCCTAGATTAAGTTTAA-AATTTCAA--T
* *
29008571 TGTTTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTTTAGGAATTTCAATTTTGT
57 T-TTTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTTAATTTT-T
29008636 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTTTAGAAATTTCAA-TTTTAAAT
1 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTTTA-AAATTTCAATTTTTAAAT
* * * * * *
29008700 TGAACCTGTTGTGAAATAGGTCAAGCCTAAATTAAGTTTAGAAATTTTAATTTTGT
65 CGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTTAATTTT-T
* *
29008756 TTAAATTGAACCTGTTGTGAGATAAGTCGAGCCTAGATTAAGTTTAGAAATTTCAA-TTTTAAAT
1 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTTTA-AAATTTCAATTTTTAAAT
29008820 CGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTTAAT
65 CGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTTAAT
29008871 CGAATTTGTT
Statistics
Matches: 428, Mismatches: 43, Indels: 33
0.85 0.09 0.07
Matches are distributed among these distances:
119 15 0.04
120 194 0.45
121 52 0.12
122 6 0.01
123 10 0.02
124 36 0.08
125 4 0.01
127 3 0.01
128 35 0.08
129 54 0.13
130 19 0.04
ACGTcount: A:0.32, C:0.12, G:0.19, T:0.37
Consensus pattern (119 bp):
TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTTTAAAATTTCAATTTTTAAATC
GAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTTAATTTTT
Found at i:29009094 original size:13 final size:13
Alignment explanation
Indices: 29009073--29009106 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
29009063 TAGACACCTC
29009073 TAAAATAAAA-AA
1 TAAAATAAAATAA
29009085 TAATAATAAAATAA
1 TAA-AATAAAATAA
29009099 TAAAATAA
1 TAAAATAA
29009107 TTAAAAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 3 0.15
13 12 0.60
14 5 0.25
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
TAAAATAAAATAA
Found at i:29009114 original size:19 final size:18
Alignment explanation
Indices: 29009073--29009122 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 18
29009063 TAGACACCTC
29009073 TAAAATAAAAAATAATAA
1 TAAAATAAAAAATAATAA
29009091 TAAAATAATAAAATAATTAA
1 TAAAATAA-AAAATAA-TAA
29009111 -AAAATTAAAAAA
1 TAAAA-TAAAAAA
29009123 AGAAAAGAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
18 8 0.28
19 15 0.52
20 6 0.21
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (18 bp):
TAAAATAAAAAATAATAA
Found at i:29010281 original size:28 final size:27
Alignment explanation
Indices: 29010229--29010283 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
29010219 TCCTTTTTTT
* *
29010229 TATTTTTTTTATTTTTTGTTTTTGAAA
1 TATTTTTTTTATTTTTTGATCTTGAAA
*
29010256 TATTTTTTTTGTTTTTATGATCTTGAAA
1 TATTTTTTTTATTTTT-TGATCTTGAAA
29010284 ATATGTTATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 15 0.62
28 9 0.38
ACGTcount: A:0.20, C:0.02, G:0.09, T:0.69
Consensus pattern (27 bp):
TATTTTTTTTATTTTTTGATCTTGAAA
Found at i:29017608 original size:20 final size:18
Alignment explanation
Indices: 29017583--29017678 Score: 61
Period size: 20 Copynumber: 4.9 Consensus size: 18
29017573 TTTTTGTCAT
29017583 TTTTTATTATTTAATTATTA
1 TTTTTATT-TTTAATT-TTA
29017603 TTTTTA-TTTT-ATTTTA
1 TTTTTATTTTTAATTTTA
* * *
29017619 TTTTTTATTATCATATTTTC
1 -TTTTTATTTTTA-ATTTTA
*
29017639 TATTTTATTTCTAATTATTA
1 T-TTTTATTTTTAATT-TTA
29017659 TTTTTTATATTTTACATTTT
1 -TTTTTAT-TTTTA-ATTTT
29017679 TTATTCGAGG
Statistics
Matches: 59, Mismatches: 8, Indels: 17
0.70 0.10 0.20
Matches are distributed among these distances:
16 3 0.05
17 9 0.15
18 5 0.08
19 5 0.08
20 27 0.46
21 7 0.12
22 3 0.05
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTTTATTTTTAATTTTA
Found at i:29017617 original size:32 final size:33
Alignment explanation
Indices: 29017562--29017657 Score: 94
Period size: 32 Copynumber: 3.0 Consensus size: 33
29017552 ATGCTAATGC
*
29017562 AATTATCTATTTTT-TTGTCATTTTTTATTATTT
1 AATTATCTATTTTTATT-TTATTTTTTATTATTT
29017595 AATTAT-TATTTTTATTTTA--TTTTATT-TTT
1 AATTATCTATTTTTATTTTATTTTTTATTATTT
* * *
29017624 TATTATCATATTTTCTATTTTATTTCTAATTATT
1 AATTATC-TATTTT-TATTTTATTTTTTATTATT
29017658 ATTTTTTATA
Statistics
Matches: 52, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
29 8 0.15
30 7 0.13
31 6 0.12
32 16 0.31
33 8 0.15
34 5 0.10
35 2 0.04
ACGTcount: A:0.24, C:0.05, G:0.01, T:0.70
Consensus pattern (33 bp):
AATTATCTATTTTTATTTTATTTTTTATTATTT
Found at i:29017619 original size:27 final size:27
Alignment explanation
Indices: 29017581--29017672 Score: 73
Period size: 27 Copynumber: 3.2 Consensus size: 27
29017571 TTTTTTTGTC
29017581 ATTTT-TTATTATTTAATTATTATTTT-T
1 ATTTTATT-TTATTT-ATTATTATTTTAT
*
29017608 ATTTTATTTTATTTTTTATTATCATATTTTCT
1 ATTTTATTTTA---TTTATTAT--TATTTTAT
*
29017640 ATTTTATTTCTAATTATTATT-TTTTAT
1 ATTTTATTT-TATTTATTATTATTTTAT
29017667 ATTTTA
1 ATTTTA
29017673 CATTTTTTAT
Statistics
Matches: 55, Mismatches: 2, Indels: 16
0.75 0.03 0.22
Matches are distributed among these distances:
27 19 0.35
28 3 0.05
29 5 0.09
30 10 0.18
31 6 0.11
32 10 0.18
33 2 0.04
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (27 bp):
ATTTTATTTTATTTATTATTATTTTAT
Found at i:29017787 original size:9 final size:9
Alignment explanation
Indices: 29017773--29017806 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
29017763 GTTGTCTTAG
29017773 ATTTTTATT
1 ATTTTTATT
29017782 ATTTTTTATT
1 A-TTTTTATT
*
29017792 ATTTTTTTT
1 ATTTTTATT
29017801 ATTTTT
1 ATTTTT
29017807 CTATTTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 14 0.61
10 9 0.39
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (9 bp):
ATTTTTATT
Found at i:29017789 original size:10 final size:10
Alignment explanation
Indices: 29017774--29017816 Score: 61
Period size: 10 Copynumber: 4.2 Consensus size: 10
29017764 TTGTCTTAGA
29017774 TTTTTATTAT
1 TTTTTATTAT
29017784 TTTTTATTAT
1 TTTTTATTAT
29017794 TTTTT-TTAT
1 TTTTTATTAT
29017803 TTTTCTATTTAT
1 TTTT-TA-TTAT
29017815 TT
1 TT
29017817 AATGTCATGT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
9 8 0.27
10 16 0.53
12 6 0.20
ACGTcount: A:0.16, C:0.02, G:0.00, T:0.81
Consensus pattern (10 bp):
TTTTTATTAT
Found at i:29017797 original size:19 final size:21
Alignment explanation
Indices: 29017773--29017816 Score: 65
Period size: 19 Copynumber: 2.2 Consensus size: 21
29017763 GTTGTCTTAG
29017773 ATTTTTATTATTTTT-TA-TT
1 ATTTTTATTATTTTTCTATTT
*
29017792 ATTTTTTTTATTTTTCTATTT
1 ATTTTTATTATTTTTCTATTT
29017813 ATTT
1 ATTT
29017817 AATGTCATGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 14 0.64
20 2 0.09
21 6 0.27
ACGTcount: A:0.18, C:0.02, G:0.00, T:0.80
Consensus pattern (21 bp):
ATTTTTATTATTTTTCTATTT
Found at i:29017911 original size:18 final size:17
Alignment explanation
Indices: 29017868--29017928 Score: 65
Period size: 16 Copynumber: 3.7 Consensus size: 17
29017858 ATATATTCGA
29017868 ATTATTATTTTTTT-TT
1 ATTATTATTTTTTTATT
* *
29017884 ATCATCATTTTTTTATCT
1 ATTATTATTTTTTTAT-T
*
29017902 ATTATTATTTATTTA-T
1 ATTATTATTTTTTTATT
29017918 -TTATTATTTTT
1 ATTATTATTTTT
29017929 ATTGAGTAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
15 10 0.27
16 13 0.35
17 1 0.03
18 13 0.35
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (17 bp):
ATTATTATTTTTTTATT
Found at i:29019010 original size:2 final size:2
Alignment explanation
Indices: 29019003--29019043 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
29018993 CAGGTTGGCG
29019003 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
29019044 TTATAAAATC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:29019662 original size:18 final size:18
Alignment explanation
Indices: 29019621--29019663 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
29019611 TAATTATTCA
* *
29019621 ATTAATTAATTTTTAATT
1 ATTATTTAATTTTGAATT
* *
29019639 AATATTTAATTTTGATTT
1 ATTATTTAATTTTGAATT
29019657 ATTATTT
1 ATTATTT
29019664 GTCAAAATTT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (18 bp):
ATTATTTAATTTTGAATT
Found at i:29020659 original size:211 final size:211
Alignment explanation
Indices: 29020290--29020714 Score: 690
Period size: 211 Copynumber: 2.0 Consensus size: 211
29020280 GTAGCAATAT
* *
29020290 TATCAATGTGGGAATCCATTATCCTTAAGAATATTAAAAATAAATTGAGATAGAATTGAAAATTT
1 TATCAATGTGGGAATCCATTATCCTTAAGAATATTAAAAATAAACTGAGAAAGAATTGAAAATTT
* * * *
29020355 AATAAAACAAATAAAATAGTAAAAAGTTTGAGGTATTGTATCACTATCTTTATGGATAATTTTTG
66 AATAAAACAAATAAAATAGTAAAAAGTTTGAGGCATGGTATCACTATCCTTATGGATAATTTTTA
* * * * * *
29020420 CTATTTTAGAGTATAAGACTCGGTGCAAAAGGACTATAGCGGTTA-TCTTCAAGGATTCAACAGA
131 CCATTTTAGAGTACAAGACTCAGTGCAAAAGGACTATAACGGTTATTCTCCAA-GATTCAACAAA
29020484 CCCTTCCTTATATTTTG
195 CCCTTCCTTATATTTTG
29020501 TATCAATGTGGGAATCCATTATCCTTAAGAATATTAAAAATAAACTGAGAAAGAATTGAAAATTT
1 TATCAATGTGGGAATCCATTATCCTTAAGAATATTAAAAATAAACTGAGAAAGAATTGAAAATTT
* *
29020566 AATAAAACAAATAAAATAGTAAAAAGTTTGAGGCGTGGTATCATTATCCTTATGGATAATTTTTA
66 AATAAAACAAATAAAATAGTAAAAAGTTTGAGGCATGGTATCACTATCCTTATGGATAATTTTTA
* *
29020631 CCCTTTTGGAGTACAAGACTCAGTGCAAAAGGACTATAACGGTTATTCTCCAAGATTCAACAAAC
131 CCATTTTAGAGTACAAGACTCAGTGCAAAAGGACTATAACGGTTATTCTCCAAGATTCAACAAAC
29020696 CCTTCCTTATATTTTG
196 CCTTCCTTATATTTTG
29020712 TAT
1 TAT
29020715 AAACTAGTAA
Statistics
Matches: 197, Mismatches: 16, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
211 191 0.97
212 6 0.03
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.33
Consensus pattern (211 bp):
TATCAATGTGGGAATCCATTATCCTTAAGAATATTAAAAATAAACTGAGAAAGAATTGAAAATTT
AATAAAACAAATAAAATAGTAAAAAGTTTGAGGCATGGTATCACTATCCTTATGGATAATTTTTA
CCATTTTAGAGTACAAGACTCAGTGCAAAAGGACTATAACGGTTATTCTCCAAGATTCAACAAAC
CCTTCCTTATATTTTG
Found at i:29024308 original size:4 final size:4
Alignment explanation
Indices: 29024299--29024332 Score: 59
Period size: 4 Copynumber: 8.5 Consensus size: 4
29024289 AATTTGCACC
*
29024299 TTCT TTCT TTCT TTCG TTCT TTCT TTCT TTCT TT
1 TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TT
29024333 TCTTCGTTGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.00, C:0.24, G:0.03, T:0.74
Consensus pattern (4 bp):
TTCT
Found at i:29026705 original size:39 final size:39
Alignment explanation
Indices: 29026662--29026744 Score: 148
Period size: 39 Copynumber: 2.1 Consensus size: 39
29026652 AATTTACATT
*
29026662 AATCACTATTCTAATTATAATTCTAGGAATAACTTTACC
1 AATCACTATTCTAATTATAATTCTAAGAATAACTTTACC
29026701 AATCACTATTCTAATTATAATTCTAAGAATAACTTTACC
1 AATCACTATTCTAATTATAATTCTAAGAATAACTTTACC
*
29026740 CATCA
1 AATCA
29026745 AAAGTGGATG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.40, C:0.19, G:0.04, T:0.37
Consensus pattern (39 bp):
AATCACTATTCTAATTATAATTCTAAGAATAACTTTACC
Found at i:29026790 original size:27 final size:27
Alignment explanation
Indices: 29026727--29026791 Score: 85
Period size: 27 Copynumber: 2.4 Consensus size: 27
29026717 ATAATTCTAA
**
29026727 GAATAACTTTACCCATCAAAAGTGGAT
1 GAATAACTTTACCCATCAAAAGTAAAT
* *
29026754 GAATACCTTTACCCATCAAGAGTAAAT
1 GAATAACTTTACCCATCAAAAGTAAAT
*
29026781 GTATAACTTTA
1 GAATAACTTTA
29026792 GTTATACCCA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.40, C:0.18, G:0.12, T:0.29
Consensus pattern (27 bp):
GAATAACTTTACCCATCAAAAGTAAAT
Found at i:29032189 original size:117 final size:117
Alignment explanation
Indices: 29032026--29032249 Score: 432
Period size: 117 Copynumber: 1.9 Consensus size: 117
29032016 AATTGTTTTG
29032026 CCAAACATCTTATGTATAAAAAAGAGTTTATGAATTTACCAAATCACTTTATAATAGTTTTTAAA
1 CCAAACATCTTATGTATAAAAAAGAGTTTATGAATTTACCAAATCACTTTATAATAGTTTTTAAA
29032091 TTAAAAAAATTTATTTTAATTATTAATTAT-AAATTTTATTTTATATAAAAA
66 TTAAAAAAATTTATTTTAATTATTAATTATAAAATTTTATTTTATATAAAAA
29032142 NCCAAACATCTTATGTATAAAAAAGAGTTTATGAATTTACCAAATCACTTTATAATAGTTTTTAA
1 -CCAAACATCTTATGTATAAAAAAGAGTTTATGAATTTACCAAATCACTTTATAATAGTTTTTAA
29032207 ATTAAAAAAATTTATTTTAATTATTAATTATAAAATTTTATTT
65 ATTAAAAAAATTTATTTTAATTATTAATTATAAAATTTTATTT
29032250 AATTTACAAA
Statistics
Matches: 106, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
117 95 0.90
118 11 0.10
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.43
Consensus pattern (117 bp):
CCAAACATCTTATGTATAAAAAAGAGTTTATGAATTTACCAAATCACTTTATAATAGTTTTTAAA
TTAAAAAAATTTATTTTAATTATTAATTATAAAATTTTATTTTATATAAAAA
Found at i:29037613 original size:30 final size:31
Alignment explanation
Indices: 29037579--29037639 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
29037569 TTATAAAAAA
*
29037579 TTATTT-AATATAACATAAA-AATATAAATTT
1 TTATTTAAATATAACA-AAAGAATAAAAATTT
*
29037609 TTATTTAAATATAATAAAAGAATAAAAATTT
1 TTATTTAAATATAACAAAAGAATAAAAATTT
29037640 AGTAAAAAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
30 9 0.33
31 18 0.67
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (31 bp):
TTATTTAAATATAACAAAAGAATAAAAATTT
Found at i:29037640 original size:29 final size:30
Alignment explanation
Indices: 29037570--29037640 Score: 76
Period size: 29 Copynumber: 2.4 Consensus size: 30
29037560 AACTATTTAT
*
29037570 TATAAAAAATTATTTAATATAACATAAAAA
1 TATAAAAATTTATTTAATATAACATAAAAA
**
29037600 TATAAATTTTTATTTAA-ATATA-ATAAAAGA
1 TATAAAAATTTATTTAATATA-ACATAAAA-A
29037630 -ATAAAAATTTA
1 TATAAAAATTTA
29037641 GTAAAAAGTT
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
29 18 0.53
30 16 0.47
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.38
Consensus pattern (30 bp):
TATAAAAATTTATTTAATATAACATAAAAA
Found at i:29040701 original size:21 final size:22
Alignment explanation
Indices: 29040611--29040726 Score: 84
Period size: 22 Copynumber: 5.6 Consensus size: 22
29040601 ATTGTGTCAC
* *
29040611 TGATTTTTAAGTATTACGAGAT
1 TGATTTTTAAGCATTACGTGAT
* *
29040633 TAATTTTTAGGCATTAC--G--
1 TGATTTTTAAGCATTACGTGAT
* * * *
29040651 TGA--CTTAATCATTACGTTAC
1 TGATTTTTAAGCATTACGTGAT
29040671 TGATTTTTAAGCATTACGTGAT
1 TGATTTTTAAGCATTACGTGAT
** *
29040693 TGA-TTTTAAATATTATGTGAT
1 TGATTTTTAAGCATTACGTGAT
29040714 TGATTTTTAAGCA
1 TGATTTTTAAGCA
29040727 ATGCCTAAGT
Statistics
Matches: 70, Mismatches: 17, Indels: 14
0.69 0.17 0.14
Matches are distributed among these distances:
16 9 0.13
18 2 0.03
20 4 0.06
21 18 0.26
22 37 0.53
ACGTcount: A:0.30, C:0.09, G:0.16, T:0.46
Consensus pattern (22 bp):
TGATTTTTAAGCATTACGTGAT
Found at i:29040841 original size:22 final size:22
Alignment explanation
Indices: 29040796--29040898 Score: 66
Period size: 22 Copynumber: 4.7 Consensus size: 22
29040786 TCAACCTGTA
* * *
29040796 ACGTATTACTTAAAAATTAATC
1 ACGTAATACTTAAAAACTAGTC
29040818 ACGTAATACTTAAAAACTAGTC
1 ACGTAATACTTAAAAACTAGTC
** **
29040840 ACAAAATA-TCTAAAGTC-AGTC
1 ACGTAATACT-TAAAAACTAGTC
* * *
29040861 ATGTAATATTTAAAAATTAGTC
1 ACGTAATACTTAAAAACTAGTC
** *
29040883 ACACAATACTCAAAAA
1 ACGTAATACTTAAAAA
29040899 TCAATTACAC
Statistics
Matches: 60, Mismatches: 18, Indels: 6
0.71 0.21 0.07
Matches are distributed among these distances:
21 14 0.23
22 46 0.77
ACGTcount: A:0.49, C:0.16, G:0.07, T:0.29
Consensus pattern (22 bp):
ACGTAATACTTAAAAACTAGTC
Found at i:29042720 original size:14 final size:14
Alignment explanation
Indices: 29042691--29042735 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 14
29042681 TGTTGCATAA
29042691 TTTAAATATTAATAT
1 TTTAAA-ATTAATAT
29042706 TTT-AAATTAATTAT
1 TTTAAAATTAA-TAT
29042720 TTTAAAATTAAATAT
1 TTTAAAATT-AATAT
29042735 T
1 T
29042736 AATATTTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
13 5 0.19
14 8 0.30
15 12 0.44
16 2 0.07
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TTTAAAATTAATAT
Found at i:29042720 original size:20 final size:20
Alignment explanation
Indices: 29042692--29042761 Score: 78
Period size: 20 Copynumber: 3.8 Consensus size: 20
29042682 GTTGCATAAT
29042692 TTAAATATTAATATTTTAAA
1 TTAAATATTAATATTTTAAA
*
29042712 TT--A-ATT-AT-TTTAAAA
1 TTAAATATTAATATTTTAAA
*
29042727 TTAAATATTAATATTTTTAA
1 TTAAATATTAATATTTTAAA
*
29042747 TAAAATATTAATATT
1 TTAAATATTAATATT
29042762 CATTAAACTT
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
15 8 0.20
16 2 0.05
17 4 0.10
18 4 0.10
19 2 0.05
20 21 0.51
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TTAAATATTAATATTTTAAA
Found at i:29050223 original size:40 final size:41
Alignment explanation
Indices: 29050172--29050262 Score: 121
Period size: 41 Copynumber: 2.2 Consensus size: 41
29050162 TTATATAATA
* * *
29050172 TCATCTCTTTAATAT-ATTTTTAATGTCATATATTTTATTT
1 TCATTTCTTTAATATAATTTTTAATATCAAATATTTTATTT
* *
29050212 TCATTTCTTTAATATAATTTTTTATATTAAATATTTTATTT
1 TCATTTCTTTAATATAATTTTTAATATCAAATATTTTATTT
*
29050253 TAATTTCTTT
1 TCATTTCTTT
29050263 TACCTATATT
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
40 14 0.32
41 30 0.68
ACGTcount: A:0.29, C:0.08, G:0.01, T:0.63
Consensus pattern (41 bp):
TCATTTCTTTAATATAATTTTTAATATCAAATATTTTATTT
Found at i:29050308 original size:26 final size:25
Alignment explanation
Indices: 29050243--29050364 Score: 79
Period size: 26 Copynumber: 4.5 Consensus size: 25
29050233 TTATATTAAA
*
29050243 TATTTTATTTTAATTTCTTTTACCTATAT
1 TATTTTATTTTAATTTC--TTA--TATTT
**
29050272 TATATAAATTTTAATTTCTTATATTT
1 TAT-TTTATTTTAATTTCTTATATTT
29050298 TATTTTGATTTTAATTTC-TA-ATTCT
1 TATTTT-ATTTTAATTTCTTATATT-T
*
29050323 TATATATTATTTT-ATTTTTAATATATTT
1 TAT-T-TTATTTTAATTTCT--TATATTT
29050351 TATTTTAATTTTAA
1 TATTTT-ATTTTAA
29050365 CATTACAAAA
Statistics
Matches: 76, Mismatches: 6, Indels: 23
0.72 0.06 0.22
Matches are distributed among these distances:
24 3 0.04
25 11 0.14
26 26 0.34
27 8 0.11
28 10 0.13
29 6 0.08
30 12 0.16
ACGTcount: A:0.30, C:0.05, G:0.01, T:0.65
Consensus pattern (25 bp):
TATTTTATTTTAATTTCTTATATTT
Found at i:29050323 original size:32 final size:31
Alignment explanation
Indices: 29050243--29050340 Score: 96
Period size: 32 Copynumber: 3.2 Consensus size: 31
29050233 TTATATTAAA
* *
29050243 TATTTT-ATTTTAATTTCTT-T-TACCTATAT
1 TATTTTAATTTTAATTTCTTATATA-TTATTT
* * *
29050272 TATATAAATTTTAATTTCTTATATTTTATTT
1 TATTTTAATTTTAATTTCTTATATATTATTT
29050303 TGATTTTAATTTCTAA-TTCTTATATATTATTT
1 T-ATTTTAATTT-TAATTTCTTATATATTATTT
29050335 TATTTT
1 TATTTT
29050341 TAATATATTT
Statistics
Matches: 56, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
29 4 0.07
30 13 0.23
31 11 0.20
32 25 0.45
33 3 0.05
ACGTcount: A:0.28, C:0.06, G:0.01, T:0.65
Consensus pattern (31 bp):
TATTTTAATTTTAATTTCTTATATATTATTT
Found at i:29050353 original size:21 final size:21
Alignment explanation
Indices: 29050323--29050364 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
29050313 TTCTAATTCT
*
29050323 TATATATTATTTTATTTTTAA
1 TATATATTATTTTAATTTTAA
*
29050344 TATATTTTATTTTAATTTTAA
1 TATATATTATTTTAATTTTAA
29050365 CATTACAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (21 bp):
TATATATTATTTTAATTTTAA
Found at i:29051072 original size:12 final size:12
Alignment explanation
Indices: 29051049--29051078 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
29051039 AAAAGAACAA
29051049 AAAGAG-AAAAG
1 AAAGAGAAAAAG
29051060 AAAGAGAAAAAG
1 AAAGAGAAAAAG
29051072 AAAGAGA
1 AAAGAGA
29051079 GGGAGAAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 6 0.33
12 12 0.67
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (12 bp):
AAAGAGAAAAAG
Found at i:29052488 original size:26 final size:26
Alignment explanation
Indices: 29052429--29052490 Score: 81
Period size: 26 Copynumber: 2.3 Consensus size: 26
29052419 AACCAAAATT
* *
29052429 AAAACTTATATAAATTATTTTTTTTA
1 AAAACTTATATAAATTATTTTTGTCA
29052455 AAAGACTTATATAAATTA-TTTTGTCA
1 AAA-ACTTATATAAATTATTTTTGTCA
29052481 AACAACTTAT
1 AA-AACTTAT
29052491 CTATAAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
26 17 0.53
27 15 0.47
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.45
Consensus pattern (26 bp):
AAAACTTATATAAATTATTTTTGTCA
Found at i:29052572 original size:22 final size:22
Alignment explanation
Indices: 29052544--29052587 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
29052534 AGCTTAATTT
29052544 TAAAAGTTATTATTTTTCATAA
1 TAAAAGTTATTATTTTTCATAA
29052566 TAAAAGTTATTATTTTTCATAA
1 TAAAAGTTATTATTTTTCATAA
29052588 GAACTTTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.50
Consensus pattern (22 bp):
TAAAAGTTATTATTTTTCATAA
Found at i:29054445 original size:26 final size:27
Alignment explanation
Indices: 29054397--29054454 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 27
29054387 TAAATTATAA
*
29054397 AAAATTAATACTTTAAATTTAAA-AAT
1 AAAATTAATACTTTAAATATAAAGAAT
* *
29054423 TAAATTAATATTTTAAGA-ATAAAGAAT
1 AAAATTAATACTTTAA-ATATAAAGAAT
29054450 AAAAT
1 AAAAT
29054455 AAAATAATGA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
26 18 0.69
27 8 0.31
ACGTcount: A:0.59, C:0.02, G:0.03, T:0.36
Consensus pattern (27 bp):
AAAATTAATACTTTAAATATAAAGAAT
Found at i:29054561 original size:21 final size:20
Alignment explanation
Indices: 29054537--29054581 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
29054527 AAAATTAAAA
29054537 TAAATAATCATATTAAAATTT
1 TAAATAAT-ATATTAAAATTT
* *
29054558 TAAAATAATTTATTAATATTT
1 T-AAATAATATATTAAAATTT
29054579 TAA
1 TAA
29054582 TAAATTATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
20 2 0.10
21 12 0.57
22 7 0.33
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (20 bp):
TAAATAATATATTAAAATTT
Found at i:29054598 original size:16 final size:16
Alignment explanation
Indices: 29054579--29054619 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
29054569 ATTAATATTT
29054579 TAATAAAT-TATTTAAA
1 TAATAAATAT-TTTAAA
29054595 TAATAAATATTTTAAA
1 TAATAAATATTTTAAA
29054611 T--TAAATATT
1 TAATAAATATT
29054620 AAATGTTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 8 0.33
16 15 0.62
17 1 0.04
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
TAATAAATATTTTAAA
Found at i:29054604 original size:82 final size:83
Alignment explanation
Indices: 29054449--29054610 Score: 181
Period size: 82 Copynumber: 2.0 Consensus size: 83
29054439 GAATAAAGAA
* * * * *
29054449 TAAAATAAAATAATGATATTAATATTTTAATTATATATTATTAATCTTTTAAATGAAATATGAAT
1 TAAAATAAAATAATCATATTAAAATTTTAAATATATATTATTAATATTTTAAATGAAATATAAAT
* *
29054514 TATTAATATTCTAAAAAT
66 AATAAATATTCTAAAAAT
29054532 TAAAAT-AAATAATCATATTAAAATTTTAAA-ATA-ATTTATTAATATTTT-AAT-AAATTATTT
1 TAAAATAAAATAATCATATTAAAATTTTAAATATATA-TTATTAATATTTTAAATGAAA-TA--T
*
29054592 AAATAATAAATATTTTAAA
62 AAATAATAAATATTCTAAA
29054611 TTAAATATTA
Statistics
Matches: 67, Mismatches: 8, Indels: 9
0.80 0.10 0.11
Matches are distributed among these distances:
79 3 0.04
80 6 0.09
81 15 0.22
82 37 0.55
83 6 0.09
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (83 bp):
TAAAATAAAATAATCATATTAAAATTTTAAATATATATTATTAATATTTTAAATGAAATATAAAT
AATAAATATTCTAAAAAT
Found at i:29071735 original size:30 final size:29
Alignment explanation
Indices: 29071673--29071764 Score: 84
Period size: 27 Copynumber: 3.3 Consensus size: 29
29071663 AGGCATTAAA
* **
29071673 GTGTAAC-A-AAATTTTTTTGAACATGGT
1 GTGTAACAACAAATTTTTTTCAACATGAC
*
29071700 ATGTAACAACAATATTTTTTTCAACATGAC
1 GTGTAACAACAA-ATTTTTTTCAACATGAC
* * *
29071730 GTGTAATAAC--ATTGTTTTCAACATAAC
1 GTGTAACAACAAATTTTTTTCAACATGAC
29071757 GTGTAACA
1 GTGTAACA
29071765 TGTTTTTGTA
Statistics
Matches: 53, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
27 28 0.53
28 1 0.02
29 2 0.04
30 22 0.42
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (29 bp):
GTGTAACAACAAATTTTTTTCAACATGAC
Found at i:29071805 original size:27 final size:27
Alignment explanation
Indices: 29071710--29071824 Score: 101
Period size: 27 Copynumber: 4.4 Consensus size: 27
29071700 ATGTAACAAC
29071710 AATATTTTTTTCAACATGACGTGTAAT
1 AATATTTTTTTCAACATGACGTGTAAT
* * *
29071737 AACATTGTTTTCAACATAACGTGTAA-
1 AATATTTTTTTCAACATGACGTGTAAT
* * * *
29071763 CATGTTTTTGT--ACATGATGTGTAAT
1 AATATTTTTTTCAACATGACGTGTAAT
* * * *
29071788 AATTTTTTTTTCAACATGTCATGTAAC
1 AATATTTTTTTCAACATGACGTGTAAT
*
29071815 AATCTTTTTT
1 AATATTTTTT
29071825 AATCATAATA
Statistics
Matches: 67, Mismatches: 18, Indels: 6
0.74 0.20 0.07
Matches are distributed among these distances:
24 11 0.16
25 8 0.12
26 6 0.09
27 42 0.63
ACGTcount: A:0.30, C:0.12, G:0.11, T:0.46
Consensus pattern (27 bp):
AATATTTTTTTCAACATGACGTGTAAT
Found at i:29071841 original size:77 final size:78
Alignment explanation
Indices: 29071714--29071894 Score: 199
Period size: 77 Copynumber: 2.3 Consensus size: 78
29071704 AACAACAATA
* * * *
29071714 TTTTTTTCAACATGACGTGTAATAACATTGTTTTCAACATAACGTGTAACATGTTTTTGTACATG
1 TTTTTTTCAACATGACATGTAACAACATTGTTTTCAACATAACATGTAACATATTTTTGTACATG
29071779 AT-GTGTAATAATT
66 ATAG-GTAATAATT
* *
29071792 TTTTTTTCAACATGTCATGTAACAATC-TT-TTTT-AATCATAATATGTAACATATTTTTGTACA
1 TTTTTTTCAACATGACATGTAACAA-CATTGTTTTCAA-CATAACATGTAACATATTTTTGTACA
*
29071854 TGATAGGTAATAATAAC
64 TGATAGGTAATAAT--T
* * *
29071871 ATTTTTTCAACATAATATGTAACA
1 TTTTTTTCAACATGACATGTAACA
29071895 TCATGTACAC
Statistics
Matches: 87, Mismatches: 11, Indels: 9
0.81 0.10 0.08
Matches are distributed among these distances:
76 2 0.02
77 39 0.45
78 25 0.29
79 21 0.24
ACGTcount: A:0.34, C:0.12, G:0.10, T:0.44
Consensus pattern (78 bp):
TTTTTTTCAACATGACATGTAACAACATTGTTTTCAACATAACATGTAACATATTTTTGTACATG
ATAGGTAATAATT
Found at i:29071990 original size:13 final size:13
Alignment explanation
Indices: 29071974--29072021 Score: 51
Period size: 13 Copynumber: 3.4 Consensus size: 13
29071964 AATTATAAAA
29071974 AAAATTATTTTTG
1 AAAATTATTTTTG
29071987 AAAACATCTTATTTTTG
1 -AAA-A--TTATTTTTG
*
29072004 AAAATTATTTTTT
1 AAAATTATTTTTG
29072017 AAAAT
1 AAAAT
29072022 GCCCTATTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
13 13 0.43
14 3 0.10
15 2 0.07
16 3 0.10
17 9 0.30
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.50
Consensus pattern (13 bp):
AAAATTATTTTTG
Found at i:29074549 original size:20 final size:20
Alignment explanation
Indices: 29074512--29074554 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
29074502 TACTCAAATT
* *
29074512 TAATTTTATATAATATTTTA
1 TAATTTTATATAACATTTAA
* *
29074532 TAATTTTATTTGACATTTAA
1 TAATTTTATATAACATTTAA
29074552 TAA
1 TAA
29074555 AATTCAAATA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (20 bp):
TAATTTTATATAACATTTAA
Found at i:29079233 original size:24 final size:25
Alignment explanation
Indices: 29079202--29079253 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
29079192 TGGTATGATA
29079202 ACACACTAT-GTTCACTGCAACAGC
1 ACACACTATAGTTCACTGCAACAGC
*
29079226 ACACACTATATTTCACTGCAACAGC
1 ACACACTATAGTTCACTGCAACAGC
29079251 ACA
1 ACA
29079254 AAACAGGTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
24 9 0.35
25 17 0.65
ACGTcount: A:0.37, C:0.33, G:0.10, T:0.21
Consensus pattern (25 bp):
ACACACTATAGTTCACTGCAACAGC
Found at i:29106503 original size:40 final size:38
Alignment explanation
Indices: 29106446--29106540 Score: 104
Period size: 40 Copynumber: 2.4 Consensus size: 38
29106436 TTCAAGTAAA
*
29106446 TTATTATTAAAAGTTTATA-AAAAGTAT-ATTATTGTAAATT
1 TTATT-TTAAAAATTTATACAAAA-TATAATT-TT-TAAATT
29106486 TTAATTTTAAAAATTTATACAAAATATAATTTTTAAATT
1 TT-ATTTTAAAAATTTATACAAAATATAATTTTTAAATT
* *
29106525 TTCTTTAAAAAATTTA
1 TTATTTTAAAAATTTA
29106541 AATGACTTCA
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
38 12 0.24
39 8 0.16
40 19 0.39
41 10 0.20
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.48
Consensus pattern (38 bp):
TTATTTTAAAAATTTATACAAAATATAATTTTTAAATT
Found at i:29142321 original size:5 final size:5
Alignment explanation
Indices: 29142311--29142347 Score: 56
Period size: 5 Copynumber: 7.4 Consensus size: 5
29142301 AGCAGAAGGT
* *
29142311 AAAAG AAAAG AAAAG AAAAG AAAAG CATAG AAAAG AA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AA
29142348 GGGTTTGGTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.76, C:0.03, G:0.19, T:0.03
Consensus pattern (5 bp):
AAAAG
Found at i:29150077 original size:2 final size:2
Alignment explanation
Indices: 29150066--29150101 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
29150056 CAGATAGACT
29150066 GA GA GA -A GA GA GA GA GA GA GA GA GA GA GA -A GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
29150102 AAGCTTCAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
GA
Found at i:29160848 original size:14 final size:14
Alignment explanation
Indices: 29160829--29160858 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
29160819 GTTTGGTGAA
29160829 TTTTTTTTTATAAG
1 TTTTTTTTTATAAG
29160843 TTTTTTTTTATAAG
1 TTTTTTTTTATAAG
29160857 TT
1 TT
29160859 ATACTTTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.20, C:0.00, G:0.07, T:0.73
Consensus pattern (14 bp):
TTTTTTTTTATAAG
Found at i:29161698 original size:30 final size:30
Alignment explanation
Indices: 29161664--29161758 Score: 92
Period size: 30 Copynumber: 3.3 Consensus size: 30
29161654 AGCATATGTT
29161664 TTATTTAACTT-AAAATAAAAATATAAAAAC
1 TTATTTAA-TTCAAAATAAAAATATAAAAAC
** *
29161694 TTATTTAATTCAAAATAAAAGCAT--AGA-
1 TTATTTAATTCAAAATAAAAATATAAAAAC
* *
29161721 -GATTTAATTGAATAATAAAAATATAAAAAC
1 TTATTTAATTCAA-AATAAAAATATAAAAAC
29161751 TTATTTAA
1 TTATTTAA
29161759 ATTTTCATAA
Statistics
Matches: 50, Mismatches: 9, Indels: 11
0.71 0.13 0.16
Matches are distributed among these distances:
26 10 0.20
27 9 0.18
28 2 0.04
29 4 0.08
30 19 0.38
31 6 0.12
ACGTcount: A:0.56, C:0.05, G:0.04, T:0.35
Consensus pattern (30 bp):
TTATTTAATTCAAAATAAAAATATAAAAAC
Found at i:29174970 original size:9 final size:9
Alignment explanation
Indices: 29174956--29174981 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
29174946 TTATGACTAC
29174956 AATTTTAAT
1 AATTTTAAT
29174965 AATTTTAAT
1 AATTTTAAT
29174974 AATTTTAA
1 AATTTTAA
29174982 ATTGAATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (9 bp):
AATTTTAAT
Found at i:29206249 original size:11 final size:11
Alignment explanation
Indices: 29206233--29206267 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
29206223 ATGATAGAAT
29206233 ATTTTAAAAAA
1 ATTTTAAAAAA
*
29206244 ATTTT-AAAAT
1 ATTTTAAAAAA
29206254 ATTTTAAAAAA
1 ATTTTAAAAAA
29206265 ATT
1 ATT
29206268 AAATAAGTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 9 0.43
11 12 0.57
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (11 bp):
ATTTTAAAAAA
Found at i:29210207 original size:40 final size:40
Alignment explanation
Indices: 29210152--29210230 Score: 140
Period size: 40 Copynumber: 2.0 Consensus size: 40
29210142 TTGGCTATTT
*
29210152 TTCACCTTAGTGGGGTTTTCAACCTTGCCAAGATTGGTGA
1 TTCACCTTAGTGGGGTTTTCAACCTCGCCAAGATTGGTGA
*
29210192 TTCACCTTAGTGGGGTTTTCAACCTCGCCACGATTGGTG
1 TTCACCTTAGTGGGGTTTTCAACCTCGCCAAGATTGGTG
29210231 TTTTTCATAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.18, C:0.23, G:0.25, T:0.34
Consensus pattern (40 bp):
TTCACCTTAGTGGGGTTTTCAACCTCGCCAAGATTGGTGA
Found at i:29212492 original size:30 final size:30
Alignment explanation
Indices: 29212434--29212489 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
29212424 TTTAGTTGAT
29212434 TTAGGATTTATTTTCTTTATTTTATTTAAA
1 TTAGGATTTATTTTCTTTATTTTATTTAAA
*
29212464 TTAGGA-TTCTTTTC-TTATTTTTATTT
1 TTAGGATTTATTTTCTTTA-TTTTATTT
29212490 TAATACTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 3 0.12
29 15 0.62
30 6 0.25
ACGTcount: A:0.21, C:0.05, G:0.07, T:0.66
Consensus pattern (30 bp):
TTAGGATTTATTTTCTTTATTTTATTTAAA
Found at i:29212771 original size:91 final size:90
Alignment explanation
Indices: 29212610--29212794 Score: 318
Period size: 91 Copynumber: 2.0 Consensus size: 90
29212600 AGGAGTAGAG
*
29212610 TTTTATTAGGATTTGGGCCTATAATACTATAAATAGGACCCTTAGGCTTAGTTACGAGACATTCA
1 TTTTATTAGGATTTGGGCATATAATACTATAAATAGGACCCTTAGGCTTAGTTACGAGACATTCA
*
29212675 GAATTGAGAGTTAATAAATAATATT
66 AAATTGAGAGTTAATAAATAATATT
*
29212700 TTNTTATTAGG-TATTGGGCATATAATACTATAAATAGGACCCTTAGGCTTAGTTACGAGATATT
1 TT-TTATTAGGAT-TTGGGCATATAATACTATAAATAGGACCCTTAGGCTTAGTTACGAGACATT
29212764 CAAAATTGAGAGTTAATAAATAATATT
64 CAAAATTGAGAGTTAATAAATAATATT
29212791 TTTT
1 TTTT
29212795 TAAGCATGAG
Statistics
Matches: 90, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
90 5 0.06
91 85 0.94
ACGTcount: A:0.36, C:0.10, G:0.17, T:0.37
Consensus pattern (90 bp):
TTTTATTAGGATTTGGGCATATAATACTATAAATAGGACCCTTAGGCTTAGTTACGAGACATTCA
AAATTGAGAGTTAATAAATAATATT
Found at i:29212936 original size:40 final size:40
Alignment explanation
Indices: 29212888--29212966 Score: 133
Period size: 40 Copynumber: 2.0 Consensus size: 40
29212878 TTGGTTATTT
*
29212888 TTCACCTTAGTGGGGTTTTCAACCTTGCCA-AGATTGGTGA
1 TTCACCTTAGTGGGGTTTTCAACCTCGCCACA-ATTGGTGA
29212928 TTCACCTTAGTGGGGTTTTCAACCTCGCCACAATTGGTG
1 TTCACCTTAGTGGGGTTTTCAACCTCGCCACAATTGGTG
29212967 TTTTTCATAA
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
40 36 0.97
41 1 0.03
ACGTcount: A:0.19, C:0.23, G:0.24, T:0.34
Consensus pattern (40 bp):
TTCACCTTAGTGGGGTTTTCAACCTCGCCACAATTGGTGA
Found at i:29220888 original size:30 final size:30
Alignment explanation
Indices: 29220833--29220890 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
29220823 CCCTGTAATT
* **
29220833 TCTTTTTTACCAATTATCATGCTATGGATA
1 TCTTTTTTACCAATTAGCACCCTATGGATA
*
29220863 TCTTTTTTTCCAATTAGCACCCTATGGA
1 TCTTTTTTACCAATTAGCACCCTATGGA
29220891 CAACTTCTGT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.24, C:0.21, G:0.10, T:0.45
Consensus pattern (30 bp):
TCTTTTTTACCAATTAGCACCCTATGGATA
Found at i:29221076 original size:31 final size:31
Alignment explanation
Indices: 29221034--29221106 Score: 85
Period size: 32 Copynumber: 2.3 Consensus size: 31
29221024 TAACCTTTTA
* **
29221034 TGAGAACAAAAATG-ATCCATAGGGTGCTAAT
1 TGAGAA-AAAAAAGAATCCATAAAGTGCTAAT
*
29221065 TGAGAAAAAAAAGATATCCATAAAGTGCTGAT
1 TGAGAAAAAAAAGA-ATCCATAAAGTGCTAAT
29221097 TGAGAAAAAA
1 TGAGAAAAAA
29221107 GAAACCACAT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
30 6 0.17
31 6 0.17
32 24 0.67
ACGTcount: A:0.49, C:0.10, G:0.21, T:0.21
Consensus pattern (31 bp):
TGAGAAAAAAAAGAATCCATAAAGTGCTAAT
Found at i:29229073 original size:8 final size:8
Alignment explanation
Indices: 29229056--29229088 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
29229046 TAATAATAAT
29229056 AATG-AAA
1 AATGAAAA
29229063 AATGAAAA
1 AATGAAAA
*
29229071 AATGAAAG
1 AATGAAAA
29229079 AATGAAAA
1 AATGAAAA
29229087 AA
1 AA
29229089 GGAGAGAGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
7 4 0.17
8 19 0.83
ACGTcount: A:0.73, C:0.00, G:0.15, T:0.12
Consensus pattern (8 bp):
AATGAAAA
Found at i:29229084 original size:16 final size:15
Alignment explanation
Indices: 29229056--29229088 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
29229046 TAATAATAAT
29229056 AATGAAAAATGAAAA
1 AATGAAAAATGAAAA
29229071 AATGAAAGAATGAAAA
1 AATGAAA-AATGAAAA
29229087 AA
1 AA
29229089 GGAGAGAGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.73, C:0.00, G:0.15, T:0.12
Consensus pattern (15 bp):
AATGAAAAATGAAAA
Found at i:29240567 original size:17 final size:18
Alignment explanation
Indices: 29240541--29240574 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
29240531 CGAAGCTCTT
29240541 TTATCAAATATG-TTAAA
1 TTATCAAATATGATTAAA
*
29240558 TTATCGAATATGATTAA
1 TTATCAAATATGATTAA
29240575 TATATATGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.44, C:0.06, G:0.09, T:0.41
Consensus pattern (18 bp):
TTATCAAATATGATTAAA
Found at i:29242635 original size:31 final size:31
Alignment explanation
Indices: 29242598--29242676 Score: 158
Period size: 31 Copynumber: 2.5 Consensus size: 31
29242588 TGCCACGTCA
29242598 GCATTGCCATGTCATCAAATAGTGACATGTG
1 GCATTGCCATGTCATCAAATAGTGACATGTG
29242629 GCATTGCCATGTCATCAAATAGTGACATGTG
1 GCATTGCCATGTCATCAAATAGTGACATGTG
29242660 GCATTGCCATGTCATCA
1 GCATTGCCATGTCATCA
29242677 GTCGGTGCAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 48 1.00
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.29
Consensus pattern (31 bp):
GCATTGCCATGTCATCAAATAGTGACATGTG
Found at i:29242692 original size:31 final size:30
Alignment explanation
Indices: 29242598--29242706 Score: 123
Period size: 31 Copynumber: 3.6 Consensus size: 30
29242588 TGCCACGTCA
*
29242598 GCATTGCCATGTCATCAAATAGTGACATGTG
1 GCATTGCCATGTCATC-AATAGTGACACGTG
*
29242629 GCATTGCCATGTCATCAAATAGTGACATGTG
1 GCATTGCCATGTCATC-AATAGTGACACGTG
* *
29242660 GCATTGCCATGTCATCAGTCGGTG-CAACGTG
1 GCATTGCCATGTCATCAAT-AGTGAC-ACGTG
*
29242691 GCA-TGCCACGTCATCA
1 GCATTGCCATGTCATCA
29242707 TCTCAACACC
Statistics
Matches: 72, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
30 15 0.21
31 57 0.79
ACGTcount: A:0.26, C:0.24, G:0.24, T:0.27
Consensus pattern (30 bp):
GCATTGCCATGTCATCAATAGTGACACGTG
Found at i:29247515 original size:42 final size:41
Alignment explanation
Indices: 29247446--29247536 Score: 128
Period size: 42 Copynumber: 2.2 Consensus size: 41
29247436 AACTTTGGAT
*
29247446 CAAATCAATTCAACATTGGTAGAATAAAAATAGTTAAAGAC
1 CAAATCAATTCAACATTGGCAGAATAAAAATAGTTAAAGAC
* * *
29247487 CAAATCAACTTTAACGTTGGCAGAATAAAAATAGTTAAAGAT
1 CAAATCAA-TTCAACATTGGCAGAATAAAAATAGTTAAAGAC
*
29247529 AAAATCAA
1 CAAATCAA
29247537 ACTCTGGTAA
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
41 8 0.18
42 36 0.82
ACGTcount: A:0.52, C:0.12, G:0.12, T:0.24
Consensus pattern (41 bp):
CAAATCAATTCAACATTGGCAGAATAAAAATAGTTAAAGAC
Found at i:29249045 original size:37 final size:37
Alignment explanation
Indices: 29248978--29249063 Score: 124
Period size: 37 Copynumber: 2.4 Consensus size: 37
29248968 CATCTTATGA
29248978 TTTTAATACCAAA-AAAATATTGATTACTCCAAAATC
1 TTTTAATACCAAATAAAATATTGATTACTCCAAAATC
*
29249014 TTTTAATACCAAATATAATATTGACTT-CTCCAAAATC
1 TTTTAATACCAAATAAAATATTGA-TTACTCCAAAATC
*
29249051 TTTT-ATATCAAAT
1 TTTTAATACCAAAT
29249064 TTAGAAGTTA
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
36 21 0.46
37 23 0.50
38 2 0.04
ACGTcount: A:0.43, C:0.16, G:0.02, T:0.38
Consensus pattern (37 bp):
TTTTAATACCAAATAAAATATTGATTACTCCAAAATC
Found at i:29249623 original size:2 final size:2
Alignment explanation
Indices: 29249604--29249651 Score: 69
Period size: 2 Copynumber: 23.0 Consensus size: 2
29249594 TAAATTACTG
*
29249604 TA TA TA GTA GTA TT TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA -TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
29249648 TA TA
1 TA TA
29249652 NNNNNNNNNN
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
2 38 0.88
3 5 0.12
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (2 bp):
TA
Found at i:29250542 original size:18 final size:19
Alignment explanation
Indices: 29250516--29250560 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
29250506 AAGAGACATG
*
29250516 ATAAAATTTTA-GAATAAA
1 ATAATATTTTATGAATAAA
* *
29250534 ATAATATTTTATTAATGAA
1 ATAATATTTTATGAATAAA
29250553 ATAATATT
1 ATAATATT
29250561 AAAATATTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 10 0.43
19 13 0.57
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.42
Consensus pattern (19 bp):
ATAATATTTTATGAATAAA
Found at i:29251391 original size:23 final size:22
Alignment explanation
Indices: 29251348--29251397 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
29251338 GTGGAGGATT
* **
29251348 TCAAGAGAAAAAGTGTGAAAAA
1 TCAAGAAAAAAAGTGAAAAAAA
29251370 TCAAGAAAAATAAGTGAAAAAAA
1 TCAAGAAAAA-AAGTGAAAAAAA
29251393 T-AAGA
1 TCAAGA
29251398 TTTTTCAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 13 0.54
23 11 0.46
ACGTcount: A:0.64, C:0.04, G:0.18, T:0.14
Consensus pattern (22 bp):
TCAAGAAAAAAAGTGAAAAAAA
Found at i:29252880 original size:2 final size:2
Alignment explanation
Indices: 29252875--29252901 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
29252865 GGGACACACA
29252875 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
29252902 AGGAAAAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:29255359 original size:23 final size:25
Alignment explanation
Indices: 29255313--29255364 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
29255303 TGACTAAATA
* *
29255313 TTTATTATTTTGTTAAATTCGATAT
1 TTTATGATTTTGTAAAATTCGATAT
29255338 TTTATGATTTT-TAAAATT-GATAT
1 TTTATGATTTTGTAAAATTCGATAT
29255361 TTTA
1 TTTA
29255365 AATTTTACTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 9 0.36
24 6 0.24
25 10 0.40
ACGTcount: A:0.31, C:0.02, G:0.08, T:0.60
Consensus pattern (25 bp):
TTTATGATTTTGTAAAATTCGATAT
Found at i:29257973 original size:2 final size:2
Alignment explanation
Indices: 29257966--29258008 Score: 61
Period size: 2 Copynumber: 21.5 Consensus size: 2
29257956 AAATATAATG
*
29257966 TA TA TA TA TA TA TA TA TA CA TA TA CT- TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA
29258008 T
1 T
29258009 TATCTCAATC
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
1 1 0.03
2 35 0.95
3 1 0.03
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:29258493 original size:27 final size:27
Alignment explanation
Indices: 29258442--29258493 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
29258432 ATTTCAATTT
* *
29258442 TATTGTTAAATTTTCAACTTCTGTATA
1 TATTGTCAAATTTTCAAATTCTGTATA
* *
29258469 TATTGTCAAGTTTTCAAATTTTGTA
1 TATTGTCAAATTTTCAAATTCTGTA
29258494 AAAAATGGTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.29, C:0.10, G:0.10, T:0.52
Consensus pattern (27 bp):
TATTGTCAAATTTTCAAATTCTGTATA
Found at i:29262033 original size:46 final size:47
Alignment explanation
Indices: 29261966--29262059 Score: 163
Period size: 46 Copynumber: 2.0 Consensus size: 47
29261956 TCATAACTGA
29261966 CACGTTCTTCTATACGTGCTCTTTTAATAAGACATTAACGTGT-CTT
1 CACGTTCTTCTATACGTGCTCTTTTAATAAGACATTAACGTGTGCTT
**
29262012 CACGTTCTTCTATACGTGCTCTTTTAATAAGATGTTAACGTGTGCTT
1 CACGTTCTTCTATACGTGCTCTTTTAATAAGACATTAACGTGTGCTT
29262059 C
1 C
29262060 CCATAACAGG
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
46 41 0.91
47 4 0.09
ACGTcount: A:0.22, C:0.21, G:0.15, T:0.41
Consensus pattern (47 bp):
CACGTTCTTCTATACGTGCTCTTTTAATAAGACATTAACGTGTGCTT
Found at i:29264032 original size:39 final size:38
Alignment explanation
Indices: 29263989--29264108 Score: 98
Period size: 39 Copynumber: 3.1 Consensus size: 38
29263979 GTAGCATTTG
*
29263989 GAACACCTCCATGAGAAGAAGAATTATGAGTAGTGTTCA
1 GAACACCTCCAAGAGAA-AAGAATTATGAGTAGTGTTCA
* * * * * **
29264028 GAACACTTCCAAAAGAAAAAAAGTTATGAATAGTATTTG
1 GAACACCTCCAAGAGAAAAGAA-TTATGAGTAGTGTTCA
* * *
29264067 GAACACC-CCAAGGGGAAAAAGCATTATGAGTAATGTTCA
1 GAACACCTCCAA-GAG-AAAAGAATTATGAGTAGTGTTCA
29264106 GAA
1 GAA
29264109 TAGCTCTAGA
Statistics
Matches: 60, Mismatches: 18, Indels: 6
0.71 0.21 0.07
Matches are distributed among these distances:
38 8 0.13
39 47 0.78
40 5 0.08
ACGTcount: A:0.43, C:0.14, G:0.21, T:0.22
Consensus pattern (38 bp):
GAACACCTCCAAGAGAAAAGAATTATGAGTAGTGTTCA
Done.