Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D10
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: 65706892
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 869813 characters in sequence are not A, C, G, or T
File 181 of 218
Found at i:54387093 original size:28 final size:28
Alignment explanation
Indices: 54387060--54387114 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
54387050 GTCACACGGT
*
54387060 CGTGTCTCACACACGGCCAGCCACACGC
1 CGTGTCTCACACACGACCAGCCACACGC
*
54387088 CGTGTCTCGCACACGACCAGCCACACG
1 CGTGTCTCACACACGACCAGCCACACG
54387115 GTCGGCCACA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.22, C:0.45, G:0.22, T:0.11
Consensus pattern (28 bp):
CGTGTCTCACACACGACCAGCCACACGC
Found at i:54389110 original size:23 final size:23
Alignment explanation
Indices: 54389066--54389117 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 23
54389056 ATTACTACTG
*
54389066 TATATACATGCGCATAGGTTTTT
1 TATATACATGCACATAGGTTTTT
*
54389089 TATATA-ATGCACATATGTTTTT
1 TATATACATGCACATAGGTTTTT
54389111 TAGTATA
1 TA-TATA
54389118 TGTTTATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
22 16 0.62
23 10 0.38
ACGTcount: A:0.31, C:0.10, G:0.13, T:0.46
Consensus pattern (23 bp):
TATATACATGCACATAGGTTTTT
Found at i:54389143 original size:25 final size:25
Alignment explanation
Indices: 54389115--54389164 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
54389105 GTTTTTTAGT
54389115 ATATG-TTTATATATATATTTTATTC
1 ATATGTTTTATATATA-ATTTTATTC
* *
54389140 ATATGTTTTATTTTTAATTTTATTC
1 ATATGTTTTATATATAATTTTATTC
54389165 CCTAATTTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 14 0.64
26 8 0.36
ACGTcount: A:0.28, C:0.04, G:0.04, T:0.64
Consensus pattern (25 bp):
ATATGTTTTATATATAATTTTATTC
Found at i:54390472 original size:9 final size:8
Alignment explanation
Indices: 54390453--54390495 Score: 50
Period size: 9 Copynumber: 4.9 Consensus size: 8
54390443 AAAATAACTC
54390453 AAAATTAA
1 AAAATTAA
54390461 AAAATATAA
1 AAAAT-TAA
54390470 AAAATTCATA
1 AAAATT-A-A
54390480 AAAATATAA
1 AAAAT-TAA
54390489 AAAATTA
1 AAAATTA
54390496 CATGAAGTAC
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
8 8 0.26
9 15 0.48
10 7 0.23
11 1 0.03
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (8 bp):
AAAATTAA
Found at i:54400926 original size:44 final size:44
Alignment explanation
Indices: 54400856--54400963 Score: 148
Period size: 44 Copynumber: 2.5 Consensus size: 44
54400846 CTAAAGTACC
* * * *
54400856 TTTCCCAC-AAATGCCGCTAAAGAACATGACCTTTAGTGGCGCT
1 TTTCCCACAAAACGCCGCTAAACAACATGACCTTTAGCGGCACT
54400899 TTTCCCACAAAACGCCGCTAAACAACATGACCTTTAGCGGCACT
1 TTTCCCACAAAACGCCGCTAAACAACATGACCTTTAGCGGCACT
* *
54400943 TTTACTA-AAAACGCCGCTAAA
1 TTTCCCACAAAACGCCGCTAAA
54400964 GGTCATATTC
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
43 22 0.38
44 36 0.62
ACGTcount: A:0.32, C:0.30, G:0.15, T:0.23
Consensus pattern (44 bp):
TTTCCCACAAAACGCCGCTAAACAACATGACCTTTAGCGGCACT
Found at i:54401433 original size:66 final size:65
Alignment explanation
Indices: 54401316--54401453 Score: 170
Period size: 66 Copynumber: 2.1 Consensus size: 65
54401306 TCATATTCTG
* * * * *
54401316 AAGTTGTAGCTGGAGTTCGTCATGTTTTCTACTTGCCTCTGCTTCCCTCGATGTTGCCTCCGCTT
1 AAGTTGTAGCTGGAATTCGTCATATTTTCTA-TTGCCTCTACTTCCCTCGATGCTGCCTCCACTT
54401381 T
65 T
* **
54401382 AAGTTGTAGCTGGAATTCTTCATATTTTCT-TTGAGCCTCTACTTCTGTCGATGCTGCCTCCACT
1 AAGTTGTAGCTGGAATTCGTCATATTTTCTATT--GCCTCTACTTCCCTCGATGCTGCCTCCACT
54401446 TT
64 TT
54401448 AAGTTG
1 AAGTTG
54401454 AGCAATTTGC
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
64 2 0.03
66 60 0.97
ACGTcount: A:0.14, C:0.25, G:0.20, T:0.41
Consensus pattern (65 bp):
AAGTTGTAGCTGGAATTCGTCATATTTTCTATTGCCTCTACTTCCCTCGATGCTGCCTCCACTTT
Found at i:54404933 original size:16 final size:15
Alignment explanation
Indices: 54404912--54404942 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
54404902 TCAGAAATAA
54404912 ATAAATAAACAAAAAT
1 ATAAATAAA-AAAAAT
54404928 ATAAATAAAAAAAAT
1 ATAAATAAAAAAAAT
54404943 TATTAAAAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.19
Consensus pattern (15 bp):
ATAAATAAAAAAAAT
Found at i:54405301 original size:8 final size:8
Alignment explanation
Indices: 54405290--54405314 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
54405280 GTACCTGCGT
54405290 AGCAAACA
1 AGCAAACA
54405298 AGCAAACA
1 AGCAAACA
54405306 AGCAAACA
1 AGCAAACA
54405314 A
1 A
54405315 CCATGCATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.64, C:0.24, G:0.12, T:0.00
Consensus pattern (8 bp):
AGCAAACA
Found at i:54410082 original size:22 final size:23
Alignment explanation
Indices: 54410048--54410092 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
54410038 TTAAGGTTTT
**
54410048 AAAATTAATTAAATCAATTATTA
1 AAAATTAATTAAAAAAATTATTA
*
54410071 AAAATTTA-TAAAAAAATTATTA
1 AAAATTAATTAAAAAAATTATTA
54410093 TTAAAAATAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (23 bp):
AAAATTAATTAAAAAAATTATTA
Found at i:54421332 original size:24 final size:25
Alignment explanation
Indices: 54421304--54421359 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 25
54421294 ATGAAAATAT
54421304 TATTAATAAATAAATA-AATTTATA
1 TATTAATAAATAAATATAATTTATA
* * *
54421328 TATT-ATATATTAATATTATTTATA
1 TATTAATAAATAAATATAATTTATA
54421352 TATATAAT
1 TAT-TAAT
54421360 GTTAATTTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 9 0.35
24 14 0.54
25 1 0.04
26 2 0.08
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (25 bp):
TATTAATAAATAAATATAATTTATA
Found at i:54425863 original size:21 final size:22
Alignment explanation
Indices: 54425834--54425880 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
54425824 CAGAAGGAGT
*
54425834 GAGTAGTACTTCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
54425856 GAGT-GTACTCCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
54425877 GAGT
1 GAGT
54425881 TTGAGCAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.19, G:0.38, T:0.21
Consensus pattern (22 bp):
GAGTAGTACTCCGCAGCAGGTG
Found at i:54430659 original size:20 final size:20
Alignment explanation
Indices: 54430634--54430675 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 20
54430624 AAGTTTAGTA
54430634 TTTACT-TTTTTATTAAAATG
1 TTTACTATTTTT-TTAAAATG
54430654 TTTACTCATTTTTTTAAAATG
1 TTTACT-ATTTTTTTAAAATG
54430675 T
1 T
54430676 AATTTAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 6 0.30
21 9 0.45
22 5 0.25
ACGTcount: A:0.29, C:0.07, G:0.05, T:0.60
Consensus pattern (20 bp):
TTTACTATTTTTTTAAAATG
Found at i:54430956 original size:63 final size:63
Alignment explanation
Indices: 54430820--54431004 Score: 172
Period size: 63 Copynumber: 2.9 Consensus size: 63
54430810 TGGTACTGTT
* * * * * * * ** * * *
54430820 AATATAAAGTACCTTAATAAAACACATATTGATAGTTTAAGTACGACATTGGATAATTTGTGAA
1 AATACAAA-TACCATAATAAAACACATATTAATAGTTCAAATACCAAATTAAACATTTTATGAA
* ** **
54430884 CATACAAATACCATAATAAAATGCATATTAATAGTTCAGGTACCAAATTAAACATTTTATGAA
1 AATACAAATACCATAATAAAACACATATTAATAGTTCAAATACCAAATTAAACATTTTATGAA
* ** *
54430947 AATATAAATACCATAATAAAACACATATTGGTAGTTCAAATACCACATTAAACATTTT
1 AATACAAATACCATAATAAAACACATATTAATAGTTCAAATACCAAATTAAACATTTT
54431005 CAATACTACA
Statistics
Matches: 97, Mismatches: 24, Indels: 1
0.80 0.20 0.01
Matches are distributed among these distances:
63 91 0.94
64 6 0.06
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (63 bp):
AATACAAATACCATAATAAAACACATATTAATAGTTCAAATACCAAATTAAACATTTTATGAA
Found at i:54437398 original size:21 final size:21
Alignment explanation
Indices: 54437372--54437412 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
54437362 ATCTGCTCAA
* *
54437372 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
54437393 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
54437413 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:54441643 original size:23 final size:22
Alignment explanation
Indices: 54441617--54441660 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
54441607 TTTCAAGGCT
54441617 TTAAA-ACTATAAATTACTATAGA
1 TTAAACACTAT-AATT-CTATAGA
54441640 TTAAAGCACTATAATTCTATA
1 TTAAA-CACTATAATTCTATA
54441661 CCAGTCTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 10 0.53
24 4 0.21
25 5 0.26
ACGTcount: A:0.48, C:0.11, G:0.05, T:0.36
Consensus pattern (22 bp):
TTAAACACTATAATTCTATAGA
Found at i:54445438 original size:18 final size:18
Alignment explanation
Indices: 54445415--54445449 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
54445405 AAGTGTTTTT
54445415 ACTTTTGAGTTCAAAAGC
1 ACTTTTGAGTTCAAAAGC
54445433 ACTTTTGAGTTCAAAAG
1 ACTTTTGAGTTCAAAAG
54445450 ATGTCTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.34
Consensus pattern (18 bp):
ACTTTTGAGTTCAAAAGC
Found at i:54458323 original size:144 final size:144
Alignment explanation
Indices: 54458061--54458362 Score: 473
Period size: 144 Copynumber: 2.1 Consensus size: 144
54458051 CATGGAAGTT
* *
54458061 GGGATTGAACCAGAAAGCCCATTAAAATGAAGCACAAGATTGCCCAAGTTAGTCAAGTTTCCTAT
1 GGGATAGAACCAGAAAGCCCATTAAAATGAAGCACAAGATTACCCAAGTTAGTCAAGTTTCCTAT
*
54458126 GGAATCAGGGATGACACCAGTGAGATTATTGTCCGACAACTGCAAGTCGAAAAGAGATTTGAGCA
66 GGAATCAGGGATGACACCAGTGAGATTATTGTCCGACAACTGAAAGTCGAAAAGAGATTTGAGCA
54458191 TCCCTATCTCACTG
131 TCCCTATCTCACTG
* *
54458205 GGGATAGAACCAGAAAGCCCATTAAAATTAAGCACAAGATTATCCAAGTTAGTCAAGTTTCCTAT
1 GGGATAGAACCAGAAAGCCCATTAAAATGAAGCACAAGATTACCCAAGTTAGTCAAGTTTCCTAT
* * * *
54458270 GGAATGAGGGATGACACCAGTGAGATTATTGTTCG-CTAACTGAAACG-CTAAAAGCGATTTGAG
66 GGAATCAGGGATGACACCAGTGAGATTATTGTCCGAC-AACTGAAA-GTCGAAAAGAGATTTGAG
* *
54458333 CATTCCTATCTCATTG
129 CATCCCTATCTCACTG
54458349 GGGATAGAACCAGA
1 GGGATAGAACCAGA
54458363 GAGATTATTA
Statistics
Matches: 145, Mismatches: 11, Indels: 4
0.91 0.07 0.03
Matches are distributed among these distances:
143 1 0.01
144 143 0.99
145 1 0.01
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.24
Consensus pattern (144 bp):
GGGATAGAACCAGAAAGCCCATTAAAATGAAGCACAAGATTACCCAAGTTAGTCAAGTTTCCTAT
GGAATCAGGGATGACACCAGTGAGATTATTGTCCGACAACTGAAAGTCGAAAAGAGATTTGAGCA
TCCCTATCTCACTG
Found at i:54460689 original size:217 final size:215
Alignment explanation
Indices: 54460301--54460929 Score: 945
Period size: 217 Copynumber: 2.9 Consensus size: 215
54460291 TCAAGAGGAA
** * * * * * *
54460301 ATTTGGTTAAACGTGAAATCGAAACCCAGCACATTAGGGCACGTTTCTCGAATTTCTAAATGCAA
1 ATTTGGTCGAACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAA
* *
54460366 AACATTGCCTTATTTTTGAAAAGTTTTTAAAAAGATATTTAGCTATTTGATCGAACGAGAAATCG
66 AACATTGCCTTA-TTTTGAAAA-TTTTTAAAAGGATATTTAGCTATTTGGTCGAACGAGAAATCG
** *
54460431 AAACCCAGTACCTTAGGGCACACTCCTCGAATTTCCAAACGCAAAACATTGCCTTATTTTGAATT
129 AAACCCAGTACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAAAACATTGCCTTATTTTGAA-A
**
54460496 TTTTTTTAAAAGGATATTTAGCT
193 AGTTTTTAAAAGGATATTTAGCT
54460519 ATTTGGTCGAACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAA
1 ATTTGGTCGAACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAA
* * * *
54460584 AATATTGCCTTATTTTGAAAATTTTTGAAAAGGATATTAAG-TCATTTGGTGGAACGAGAAATCA
66 AACATTGCCTTATTTTGAAAATTTTT-AAAAGGATATTTAGCT-ATTTGGTCGAACGAGAAATCG
* *
54460648 AAACCCAATACCTTAGGGCACGTTCCTCGAATTTTCAAACGCAAAACATTGCCTTATTTTTGAAA
129 AAACCCAGTACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAAAACATTGCCTTA-TTTTGAAA
54460713 AGTTTTTAAAAGGATATTTAGCT
193 AGTTTTTAAAAGGATATTTAGCT
*
54460736 ATTTGGTCGAACGAGAAATCGAAACCCAGTACCTTAGGGCACATTCCTCGAATTTCCAAACGCAA
1 ATTTGGTCGAACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAA
* *
54460801 AACATTGCCTTATTTTGAAATTTTTTTTAAAAGAATATTTAGCTATTTGGTCGAACGAGAAATCG
66 AACATTGCCTTATTTTGAAA--ATTTTTAAAAGGATATTTAGCTATTTGGTCGAACGAGAAATCG
* *
54460866 AAACCCAGTACCTTAGGGCACGTTCCTCGAATTTCCAAACGTAAAATATTGCCTTATTTTGAAA
129 AAACCCAGTACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAAAACATTGCCTTATTTTGAAA
54460930 TATTTTCCTT
Statistics
Matches: 373, Mismatches: 32, Indels: 13
0.89 0.08 0.03
Matches are distributed among these distances:
216 6 0.02
217 203 0.54
218 158 0.42
219 6 0.02
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (215 bp):
ATTTGGTCGAACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAA
AACATTGCCTTATTTTGAAAATTTTTAAAAGGATATTTAGCTATTTGGTCGAACGAGAAATCGAA
ACCCAGTACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAAAACATTGCCTTATTTTGAAAAGT
TTTTAAAAGGATATTTAGCT
Found at i:54460894 original size:326 final size:327
Alignment explanation
Indices: 54460301--54460935 Score: 1112
Period size: 326 Copynumber: 1.9 Consensus size: 327
54460291 TCAAGAGGAA
* * * * * *
54460301 ATTTGGTTAAACGTGAAATCGAAACCCAGCACATTAGGGCACGTTTCTCGAATTTCTAAATGCAA
1 ATTTGGTGAAACGAGAAATCAAAACCCAACACATTAGGGCACGTTCCTCGAATTTCTAAACGCAA
54460366 AACATTGCCTTATTTTTGAAAAGTTTTTAAAAAGATATTTAGCTATTTGATCGAACGAGAAATCG
66 AACATTGCCTTATTTTTGAAAAGTTTTTAAAAAGATATTTAGCTATTTGATCGAACGAGAAATCG
*
54460431 AAACCCAGTACCTTAGGGCACACTCCTCGAATTTCCAAACGCAAAACATTGCCTTATTTTGAATT
131 AAACCCAGTACCTTAGGGCACACTCCTCGAATTTCCAAACGCAAAACATTGCCTTATTTTGAAAT
*
54460496 TTTTTTTAAAAGGATATTTAGCTATTTGGTCGAACGAGAAATCGAAACCCAGTACCTTAGGGCAC
196 TTTTTTTAAAAGAATATTTAGCTATTTGGTCGAACGAGAAATCGAAACCCAGTACCTTAGGGCAC
54460561 GTTCCTCGAATTTCCAAACGCAAAATATTGCCTTATTTTGAAA-ATTTTTGAAAAGGATATTAAG
261 GTTCCTCGAATTTCCAAACGCAAAATATTGCCTTATTTTGAAATATTTTTGAAAAGGATATTAAG
54460625 TC
326 TC
* * *
54460627 ATTTGGTGGAACGAGAAATCAAAACCCAATACCTTAGGGCACGTTCCTCGAATTT-TCAAACGCA
1 ATTTGGTGAAACGAGAAATCAAAACCCAACACATTAGGGCACGTTCCTCGAATTTCT-AAACGCA
* *
54460691 AAACATTGCCTTATTTTTGAAAAGTTTTTAAAAGGATATTTAGCTATTTGGTCGAACGAGAAATC
65 AAACATTGCCTTATTTTTGAAAAGTTTTTAAAAAGATATTTAGCTATTTGATCGAACGAGAAATC
*
54460756 GAAACCCAGTACCTTAGGGCACATTCCTCGAATTTCCAAACGCAAAACATTGCCTTATTTTGAAA
130 GAAACCCAGTACCTTAGGGCACACTCCTCGAATTTCCAAACGCAAAACATTGCCTTATTTTGAAA
54460821 TTTTTTTTAAAAGAATATTTAGCTATTTGGTCGAACGAGAAATCGAAACCCAGTACCTTAGGGCA
195 TTTTTTTTAAAAGAATATTTAGCTATTTGGTCGAACGAGAAATCGAAACCCAGTACCTTAGGGCA
*
54460886 CGTTCCTCGAATTTCCAAACGTAAAATATTGCCTTATTTTGAAATATTTT
260 CGTTCCTCGAATTTCCAAACGCAAAATATTGCCTTATTTTGAAATATTTT
54460936 CCTTTTTTTA
Statistics
Matches: 292, Mismatches: 15, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
325 1 0.00
326 286 0.98
327 5 0.02
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (327 bp):
ATTTGGTGAAACGAGAAATCAAAACCCAACACATTAGGGCACGTTCCTCGAATTTCTAAACGCAA
AACATTGCCTTATTTTTGAAAAGTTTTTAAAAAGATATTTAGCTATTTGATCGAACGAGAAATCG
AAACCCAGTACCTTAGGGCACACTCCTCGAATTTCCAAACGCAAAACATTGCCTTATTTTGAAAT
TTTTTTTAAAAGAATATTTAGCTATTTGGTCGAACGAGAAATCGAAACCCAGTACCTTAGGGCAC
GTTCCTCGAATTTCCAAACGCAAAATATTGCCTTATTTTGAAATATTTTTGAAAAGGATATTAAG
TC
Found at i:54460930 original size:109 final size:109
Alignment explanation
Indices: 54460301--54460935 Score: 963
Period size: 109 Copynumber: 5.8 Consensus size: 109
54460291 TCAAGAGGAA
** * * * * * *
54460301 ATTTGGTTAAACGTGAAATCGAAACCCAGCACATTAGGGCACGTTTCTCGAATTTCTAAATGCAA
1 ATTTGGTCGAACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAA
* *
54460366 AACATTGCCTTATTTTTGAAA-AGTTTTTAAAAAGATATTTAGCT
66 AACATTGCCTTA-TTTTGAAATATTTTTTAAAAGGATATTTAGCT
* **
54460410 ATTTGATCGAACGAGAAATCGAAACCCAGTACCTTAGGGCACACTCCTCGAATTTCCAAACGCAA
1 ATTTGGTCGAACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAA
* *
54460475 AACATTGCCTTATTTTGAATTTTTTTTTAAAAGGATATTTAGCT
66 AACATTGCCTTATTTTGAAATATTTTTTAAAAGGATATTTAGCT
54460519 ATTTGGTCGAACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAA
1 ATTTGGTCGAACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAA
* * *
54460584 AATATTGCCTTATTTTGAAA-ATTTTTGAAAAGGATATTAAG-T
66 AACATTGCCTTATTTTGAAATATTTTTTAAAAGGATATTTAGCT
* * * *
54460626 CATTTGGTGGAACGAGAAATCAAAACCCAATACCTTAGGGCACGTTCCTCGAATTTTCAAACGCA
1 -ATTTGGTCGAACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAATTTCCAAACGCA
*
54460691 AAACATTGCCTTATTTTTGAAA-AGTTTTTAAAAGGATATTTAGCT
65 AAACATTGCCTTA-TTTTGAAATATTTTTTAAAAGGATATTTAGCT
*
54460736 ATTTGGTCGAACGAGAAATCGAAACCCAGTACCTTAGGGCACATTCCTCGAATTTCCAAACGCAA
1 ATTTGGTCGAACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAA
* *
54460801 AACATTGCCTTATTTTGAAATTTTTTTTAAAAGAATATTTAGCT
66 AACATTGCCTTATTTTGAAATATTTTTTAAAAGGATATTTAGCT
*
54460845 ATTTGGTCGAACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAATTTCCAAACGTAA
1 ATTTGGTCGAACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAA
*
54460910 AATATTGCCTTATTTTGAAATATTTT
66 AACATTGCCTTATTTTGAAATATTTT
54460936 CCTTTTTTTA
Statistics
Matches: 478, Mismatches: 43, Indels: 10
0.90 0.08 0.02
Matches are distributed among these distances:
107 1 0.00
108 105 0.22
109 371 0.78
110 1 0.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (109 bp):
ATTTGGTCGAACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAA
AACATTGCCTTATTTTGAAATATTTTTTAAAAGGATATTTAGCT
Found at i:54461007 original size:16 final size:16
Alignment explanation
Indices: 54460986--54461016 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
54460976 ATAAATATGA
54460986 TAATGTGAACAAAAAT
1 TAATGTGAACAAAAAT
*
54461002 TAATGTGAGCAAAAA
1 TAATGTGAACAAAAA
54461017 CAAATCATTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.06, G:0.16, T:0.23
Consensus pattern (16 bp):
TAATGTGAACAAAAAT
Found at i:54462100 original size:14 final size:15
Alignment explanation
Indices: 54462059--54462091 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
54462049 AGAGTTGTAG
*
54462059 AAAATAAACA-AAAA
1 AAAATAAAAATAAAA
54462073 AAAATAAAAATAAAA
1 AAAATAAAAATAAAA
54462088 AAAA
1 AAAA
54462092 GAAAGTAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.88, C:0.03, G:0.00, T:0.09
Consensus pattern (15 bp):
AAAATAAAAATAAAA
Found at i:54464065 original size:24 final size:23
Alignment explanation
Indices: 54464038--54464086 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 23
54464028 TAGTATTTTG
* *
54464038 ATATCTAATATTTTTAAACAATTA
1 ATATATAATATTTGTAAA-AATTA
*
54464062 ATATATATTATTTGTAAAAATTA
1 ATATATAATATTTGTAAAAATTA
54464085 AT
1 AT
54464087 TTGAATATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 7 0.32
24 15 0.68
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (23 bp):
ATATATAATATTTGTAAAAATTA
Found at i:54466534 original size:21 final size:21
Alignment explanation
Indices: 54466462--54466534 Score: 58
Period size: 21 Copynumber: 3.5 Consensus size: 21
54466452 TGACAGGAGT
* *
54466462 ACACGCCGGTGT-GTCTGAGGG
1 ACACGCCCGTGTGGT-TGAGAG
* * * *
54466483 ACACACCCATGTGATTGAGAT
1 ACACGCCCGTGTGGTTGAGAG
* *
54466504 ACATGGCCGTGTGGTTGAGAG
1 ACACGCCCGTGTGGTTGAGAG
54466525 ACACGCCCGT
1 ACACGCCCGT
54466535 ATGACTGAGG
Statistics
Matches: 37, Mismatches: 14, Indels: 2
0.70 0.26 0.04
Matches are distributed among these distances:
21 36 0.97
22 1 0.03
ACGTcount: A:0.22, C:0.25, G:0.33, T:0.21
Consensus pattern (21 bp):
ACACGCCCGTGTGGTTGAGAG
Found at i:54467072 original size:139 final size:139
Alignment explanation
Indices: 54466840--54467117 Score: 547
Period size: 139 Copynumber: 2.0 Consensus size: 139
54466830 ATCCCTTAAT
54466840 TATAAGTGTTTAAGAAACACACCTGATAACGCAATTCCCAGCACCAAAGATTGACCGATTCGTCT
1 TATAAGTGTTTAAGAAACACACCTGATAACGCAATTCCCAGCACCAAAGATTGACCGATTCGTCT
54466905 CCACTCAACCAATATGAAAAACTTGACCGCTTCAAAATCTTATTGAGTGAAAATACCAAAAAGTA
66 CCACTCAACCAATATGAAAAACTTGACCGCTTCAAAATCTTATTGAGTGAAAATACCAAAAAGTA
54466970 GATGAGACC
131 GATGAGACC
54466979 TATAAGTGTTTAAGAAACACACCTGATAACGCAATTCCCAGCACCAAAGATTGACCGATTCGTCT
1 TATAAGTGTTTAAGAAACACACCTGATAACGCAATTCCCAGCACCAAAGATTGACCGATTCGTCT
*
54467044 CTACTCAACCAATATGAAAAACTTGACCGCTTCAAAATCTTATTGAGTGAAAATACCAAAAAGTA
66 CCACTCAACCAATATGAAAAACTTGACCGCTTCAAAATCTTATTGAGTGAAAATACCAAAAAGTA
54467109 GATGAGACC
131 GATGAGACC
54467118 GGAAACAGTG
Statistics
Matches: 138, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
139 138 1.00
ACGTcount: A:0.40, C:0.23, G:0.14, T:0.23
Consensus pattern (139 bp):
TATAAGTGTTTAAGAAACACACCTGATAACGCAATTCCCAGCACCAAAGATTGACCGATTCGTCT
CCACTCAACCAATATGAAAAACTTGACCGCTTCAAAATCTTATTGAGTGAAAATACCAAAAAGTA
GATGAGACC
Found at i:54470262 original size:14 final size:16
Alignment explanation
Indices: 54470229--54470269 Score: 59
Period size: 14 Copynumber: 2.7 Consensus size: 16
54470219 TCTTTCAACC
54470229 TATTTTTATAATTAAT
1 TATTTTTATAATTAAT
*
54470245 TATTTTTGTAA-T-AT
1 TATTTTTATAATTAAT
54470259 TATTTTTATAA
1 TATTTTTATAA
54470270 AAAGCATTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 12 0.52
15 1 0.04
16 10 0.43
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.63
Consensus pattern (16 bp):
TATTTTTATAATTAAT
Found at i:54472068 original size:42 final size:42
Alignment explanation
Indices: 54471854--54472213 Score: 424
Period size: 42 Copynumber: 8.4 Consensus size: 42
54471844 ACGTCGCTAA
* * *
54471854 CTTTTGCGGCGCTTATAGAAAAAAATGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGC-T-TAGGAAAAAACGCCGCTAAAGATCATGTT
*
54471898 CTTTAGCGGCGCTAAGGAAATAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTAGGAAA-AAACGCCGCTAAAGATCATGTT
* *
54471941 CTTTAGCGGCGCTTATGAAAGAAACGCCGCTACAGATCATGTT
1 CTTTAGCGGCGCTTAGGAAA-AAACGCCGCTAAAGATCATGTT
*
54471984 CTTTAGCGGAGCTTAGGAAAAAAAAAACGCCGCTACAA-ATCATGTT
1 CTTTAGCGGCGCTTAGG----AAAAAACGCCGCTA-AAGATCATGTT
*
54472030 CTTTAACGGCGCTTAGGAAAAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAGATCATGTT
* *
54472072 CTTTAGCAGCGCTTGGGAAAAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAGATCATGTT
* *
54472114 CTTTAGCGGCGCTTAGGAAGAAAGCGCCGCTAAA-AGTAATGTT
1 CTTTAGCGGCGCTTAGGAA-AAAACGCCGCTAAAGA-TCATGTT
* *
54472157 CTATAGCGGCGCTT-GGTCAAAAACGCCGCTAATAG-T-AGTGTT
1 CTTTAGCGGCGCTTAGG-AAAAAACGCCGCTAA-AGATCA-TGTT
*
54472199 CTTTAGCGGCACTTA
1 CTTTAGCGGCGCTTA
54472214 TTTCAAAAAC
Statistics
Matches: 277, Mismatches: 25, Indels: 29
0.84 0.08 0.09
Matches are distributed among these distances:
41 3 0.01
42 115 0.42
43 110 0.40
44 11 0.04
46 34 0.12
47 4 0.01
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.25
Consensus pattern (42 bp):
CTTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAGATCATGTT
Found at i:54472684 original size:21 final size:21
Alignment explanation
Indices: 54472660--54472727 Score: 91
Period size: 21 Copynumber: 3.2 Consensus size: 21
54472650 CTTCTATCGT
*
54472660 TGCTTCTCTCGCTGCGGCCTC
1 TGCTTCTCTCGCTGCAGCCTC
*
54472681 TGCTTCTCTCGCTGTAGCCTC
1 TGCTTCTCTCGCTGCAGCCTC
* * *
54472702 TGCTTCCCTCGCTGCCGCCTT
1 TGCTTCTCTCGCTGCAGCCTC
54472723 TGCTT
1 TGCTT
54472728 TAAGTTGTTG
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.01, C:0.41, G:0.21, T:0.37
Consensus pattern (21 bp):
TGCTTCTCTCGCTGCAGCCTC
Found at i:54473834 original size:42 final size:41
Alignment explanation
Indices: 54473780--54473975 Score: 148
Period size: 41 Copynumber: 4.7 Consensus size: 41
54473770 GCGCTTCAAC
*
54473780 AAAAACGCCGCTAAAACCCCTAACATTAGCGGCGCTTATCAT
1 AAAAACGCCGCTAAAACCCCTAACATTAGCAGCGCTTAT-AT
* * ** * * *
54473822 AGACACGCCGCTAAAAGTCTTAACTTTAGCATCGCTTATAT
1 AAAAACGCCGCTAAAACCCCTAACATTAGCAGCGCTTATAT
** * *
54473863 AAAAACGCCGCTAAAAGACCAAATATTAGCAGCGCTTCA-A-
1 AAAAACGCCGCTAAAACCCCTAACATTAGCAGCGCTT-ATAT
* * * *
54473903 AAAAATCGCCGCTAAATA-CCTTAACTTTAGCGGCGGTTGATA-
1 AAAAA-CGCCGCTAAA-ACCCCTAACATTAGCAGCGCTT-ATAT
* *
54473945 AAAAACGCCACTAAAACCCCCAACCATTAGC
1 AAAAACGCCGCTAAAACCCCTAA-CATTAGC
54473976 GGCGAAAGCC
Statistics
Matches: 120, Mismatches: 28, Indels: 12
0.75 0.17 0.08
Matches are distributed among these distances:
40 6 0.05
41 69 0.57
42 45 0.38
ACGTcount: A:0.38, C:0.28, G:0.14, T:0.20
Consensus pattern (41 bp):
AAAAACGCCGCTAAAACCCCTAACATTAGCAGCGCTTATAT
Found at i:54476473 original size:18 final size:18
Alignment explanation
Indices: 54476447--54476499 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
54476437 ATTTATTTAA
*
54476447 TTTAATTTAATTTTTATT
1 TTTATTTTAATTTTTATT
* *
54476465 TTTATTTTAATTATCT-GT
1 TTTATTTTAATT-TTTATT
*
54476483 ATTATTTTAATTTTTAT
1 TTTATTTTAATTTTTAT
54476500 CAGATTTAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
17 2 0.07
18 23 0.85
19 2 0.07
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (18 bp):
TTTATTTTAATTTTTATT
Found at i:54479609 original size:159 final size:159
Alignment explanation
Indices: 54479386--54479702 Score: 467
Period size: 159 Copynumber: 2.0 Consensus size: 159
54479376 ATATACCATC
* * * *
54479386 CTTTTTTGGCTTCTAGTTCTTGTACTCGTACTAGACTGAGACAAAAAAAATCACAACCCCAAATT
1 CTTTTTTAGCTTCTAGTTCTTATACTCATACTAGACTAAGACAAAAAAAATCACAACCCCAAATT
* * * * * * *
54479451 AGATTTAAATATTTTGAAATTTGACAGTAAAAAAGTGTTTACGATATAACTGTGATCTAGTTGTG
66 AGACTTAAACATTTCGAAACTTGACAATAAAAAAGTGTTTACGATATAACCGTGATCCAGTTGTG
* *
54479516 TTAGGTTGAATGCATTG-TCTTCTGTTGTT
131 TTAGGTTGAAGGCA-TGATCTTATGTTGTT
54479545 CTTTTTATAGCTTCTAGTTCTTATACTCATACTAGACTAAGA-AAAAAAAATCACAACCCCAAAT
1 CTTTTT-TAGCTTCTAGTTCTTATACTCATACTAGACTAAGACAAAAAAAATCACAACCCCAAAT
* *
54479609 TAGACTTAAACATTTCGAAACTTGATAATAAAAAAGTGTTTACGATATACCCGTGATCCAGTTGT
65 TAGACTTAAACATTTCGAAACTTGACAATAAAAAAGTGTTTACGATATAACCGTGATCCAGTTGT
54479674 GTTAGGTTGAAGGCATGATCTTATGTTGT
130 GTTAGGTTGAAGGCATGATCTTATGTTGT
54479703 AACCCTTACC
Statistics
Matches: 141, Mismatches: 15, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
158 2 0.01
159 108 0.77
160 31 0.22
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (159 bp):
CTTTTTTAGCTTCTAGTTCTTATACTCATACTAGACTAAGACAAAAAAAATCACAACCCCAAATT
AGACTTAAACATTTCGAAACTTGACAATAAAAAAGTGTTTACGATATAACCGTGATCCAGTTGTG
TTAGGTTGAAGGCATGATCTTATGTTGTT
Found at i:54481224 original size:18 final size:18
Alignment explanation
Indices: 54481201--54481239 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
54481191 CAATTGTACT
54481201 CATCATGAAAACTTTTCA
1 CATCATGAAAACTTTTCA
*
54481219 CATCATGGAAACTTTTCA
1 CATCATGAAAACTTTTCA
54481237 CAT
1 CAT
54481240 GAATGCATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.36, C:0.23, G:0.08, T:0.33
Consensus pattern (18 bp):
CATCATGAAAACTTTTCA
Found at i:54481503 original size:3 final size:3
Alignment explanation
Indices: 54481495--54481533 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
54481485 CTTTTACAAG
*
54481495 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
54481534 CATCATCATC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:54482034 original size:24 final size:23
Alignment explanation
Indices: 54481998--54482042 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
54481988 GACTGCCAGT
* *
54481998 AACCTCAATACCCTCCCCACCTA
1 AACCTCAACACCCTCACCACCTA
54482021 AACCTTCAACACCCTCACCACC
1 AACC-TCAACACCCTCACCACC
54482043 CTCACCACTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.31, C:0.53, G:0.00, T:0.16
Consensus pattern (23 bp):
AACCTCAACACCCTCACCACCTA
Found at i:54489258 original size:143 final size:143
Alignment explanation
Indices: 54489000--54489431 Score: 792
Period size: 143 Copynumber: 3.0 Consensus size: 143
54488990 ACTTGGAACT
* * *
54489000 AAGGAAATGTGCAAGTGTACAAAATCGTATCAAGTAATAAAGTGACAACTAATGTCGAGCTATCG
1 AAGGAAATGTGCAAGTGTACAAAATCGTACCAAGTAATAAAGTGACAAGTAATGTCGAGTTATCG
* *
54489065 TATCCATAGGAACTGTGAAAGAGAATATTTATGAAATGCAAATTTAAACAATTTGGTGATGGAAA
66 TATCCATAGGTACTATGAAAGAGAATATTTATGAAATGCAAATTTAAACAATTTGGTGATGGAAA
54489130 ATATGTTGATTTG
131 ATATGTTGATTTG
*
54489143 AAGGAAATGTGCAAGTGTACAAAATCATACCAAGTAATAAAGTGACAAGTAATGTCGAGTTATCG
1 AAGGAAATGTGCAAGTGTACAAAATCGTACCAAGTAATAAAGTGACAAGTAATGTCGAGTTATCG
54489208 TATCCATAGGTACTATGAAAGAGAATATTTATGAAATGCAAATTTAAACAATTTGGTGATGGAAA
66 TATCCATAGGTACTATGAAAGAGAATATTTATGAAATGCAAATTTAAACAATTTGGTGATGGAAA
54489273 ATATGTTGATTTG
131 ATATGTTGATTTG
54489286 AAGGAAATGTGCAAGTGTACAAAATCGTACCAAGTAATAAAGTGACAAGTAATGTCGAGTTATCG
1 AAGGAAATGTGCAAGTGTACAAAATCGTACCAAGTAATAAAGTGACAAGTAATGTCGAGTTATCG
* *
54489351 TATCCATAGGTACTATGAAAGAGAATATTTATGAAATGCAAATTTAAACAATTTGGTGGTGAAAA
66 TATCCATAGGTACTATGAAAGAGAATATTTATGAAATGCAAATTTAAACAATTTGGTGATGGAAA
54489416 ATATGTTGATTTG
131 ATATGTTGATTTG
54489429 AAG
1 AAG
54489432 TGGTGATATA
Statistics
Matches: 280, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
143 280 1.00
ACGTcount: A:0.41, C:0.09, G:0.21, T:0.29
Consensus pattern (143 bp):
AAGGAAATGTGCAAGTGTACAAAATCGTACCAAGTAATAAAGTGACAAGTAATGTCGAGTTATCG
TATCCATAGGTACTATGAAAGAGAATATTTATGAAATGCAAATTTAAACAATTTGGTGATGGAAA
ATATGTTGATTTG
Found at i:54493793 original size:37 final size:37
Alignment explanation
Indices: 54493743--54493816 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
54493733 TAGACTCATG
54493743 AAGTCAAACATGTCCCAAAAGTGTAGCATAAAGCTAA
1 AAGTCAAACATGTCCCAAAAGTGTAGCATAAAGCTAA
54493780 AAGTCAAACATGTCCCAAAAGTGTAGCATAAAGCTAA
1 AAGTCAAACATGTCCCAAAAGTGTAGCATAAAGCTAA
54493817 CACTCTCCTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.46, C:0.19, G:0.16, T:0.19
Consensus pattern (37 bp):
AAGTCAAACATGTCCCAAAAGTGTAGCATAAAGCTAA
Found at i:54494148 original size:82 final size:82
Alignment explanation
Indices: 54494010--54494168 Score: 309
Period size: 82 Copynumber: 1.9 Consensus size: 82
54494000 ATCAAACACT
54494010 TAACACTTACTGATTATCCGTACACTATCTCATGTTAGCATCTTTTGAAAAACACTACCACTATC
1 TAACACTTACTGATTATCCGTACACTATCTCATGTTAGCATCTTTTGAAAAACACTACCACTATC
54494075 ATATAACATATAACATA
66 ATATAACATATAACATA
*
54494092 TAACACTTACTGATTATCCGTACACTATCTCATGTTAGCATCTTTTGAAAAGCACTACCACTATC
1 TAACACTTACTGATTATCCGTACACTATCTCATGTTAGCATCTTTTGAAAAACACTACCACTATC
54494157 ATATAACATATA
66 ATATAACATATA
54494169 TTTCATGTAT
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
82 76 1.00
ACGTcount: A:0.36, C:0.23, G:0.07, T:0.33
Consensus pattern (82 bp):
TAACACTTACTGATTATCCGTACACTATCTCATGTTAGCATCTTTTGAAAAACACTACCACTATC
ATATAACATATAACATA
Found at i:54505600 original size:20 final size:20
Alignment explanation
Indices: 54505561--54505648 Score: 95
Period size: 20 Copynumber: 4.3 Consensus size: 20
54505551 TTTTGAAACA
54505561 ATTTTAAAATCAAGTTAAAATG
1 ATTTT-AAA-CAAGTTAAAATG
* *
54505583 ATTTTAACCAATTTAAAATG
1 ATTTTAAACAAGTTAAAATG
* *
54505603 ATTTTAAACAAGTCAAAATT
1 ATTTTAAACAAGTTAAAATG
* * *
54505623 ATTTCAATCAAGTTAAAATC
1 ATTTTAAACAAGTTAAAATG
54505643 ATTTTA
1 ATTTTA
54505649 GCACATCAAA
Statistics
Matches: 55, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
20 48 0.87
21 2 0.04
22 5 0.09
ACGTcount: A:0.47, C:0.09, G:0.06, T:0.39
Consensus pattern (20 bp):
ATTTTAAACAAGTTAAAATG
Found at i:54505615 original size:40 final size:41
Alignment explanation
Indices: 54505561--54505648 Score: 106
Period size: 40 Copynumber: 2.1 Consensus size: 41
54505551 TTTTGAAACA
* * * *
54505561 ATTTTAAAATCAAGTTAAAATGATTTTAACCAATTTAAAATG
1 ATTTT-AAATCAAGTCAAAATGATTTCAACCAAGTTAAAATC
* *
54505603 ATTTTAAA-CAAGTCAAAATTATTTCAATCAAGTTAAAATC
1 ATTTTAAATCAAGTCAAAATGATTTCAACCAAGTTAAAATC
54505643 ATTTTA
1 ATTTTA
54505649 GCACATCAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
40 32 0.80
41 3 0.08
42 5 0.12
ACGTcount: A:0.47, C:0.09, G:0.06, T:0.39
Consensus pattern (41 bp):
ATTTTAAATCAAGTCAAAATGATTTCAACCAAGTTAAAATC
Found at i:54505635 original size:60 final size:60
Alignment explanation
Indices: 54505568--54505682 Score: 153
Period size: 60 Copynumber: 1.9 Consensus size: 60
54505558 ACAATTTTAA
* * *
54505568 AATCAAGTTAAAATGATTTTAACCA-ATTTAAAATGATTTT-AAACAAGTCAAAATTATTTC
1 AATCAAGTTAAAATCATTTT-ACCACA-TCAAAATCATTTTCAAACAAGTCAAAATTATTTC
* *
54505628 AATCAAGTTAAAATCATTTTAGCACATCAAAATCATTTTCAAACAAGTCAGAATT
1 AATCAAGTTAAAATCATTTTACCACATCAAAATCATTTTCAAACAAGTCAAAATT
54505683 GTTCCATGCT
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
59 14 0.29
60 34 0.71
ACGTcount: A:0.46, C:0.13, G:0.07, T:0.34
Consensus pattern (60 bp):
AATCAAGTTAAAATCATTTTACCACATCAAAATCATTTTCAAACAAGTCAAAATTATTTC
Found at i:54506064 original size:42 final size:42
Alignment explanation
Indices: 54506005--54506089 Score: 161
Period size: 42 Copynumber: 2.0 Consensus size: 42
54505995 TTGGGAATCA
*
54506005 ATTAGGGGGTATAAATACCATCTTCCAAATACCTACAACAAT
1 ATTAGGGGGTATAAATACCATCTTCCAAAGACCTACAACAAT
54506047 ATTAGGGGGTATAAATACCATCTTCCAAAGACCTACAACAAT
1 ATTAGGGGGTATAAATACCATCTTCCAAAGACCTACAACAAT
54506089 A
1 A
54506090 AGAAAGCACT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.41, C:0.21, G:0.13, T:0.25
Consensus pattern (42 bp):
ATTAGGGGGTATAAATACCATCTTCCAAAGACCTACAACAAT
Found at i:54513024 original size:6 final size:6
Alignment explanation
Indices: 54513013--54513042 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
54513003 TGGAAGACCA
54513013 TCTGAT TCTGAT TCTGAT TCTGAT TCTGAT
1 TCTGAT TCTGAT TCTGAT TCTGAT TCTGAT
54513043 GTTGATGTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.17, G:0.17, T:0.50
Consensus pattern (6 bp):
TCTGAT
Found at i:54514899 original size:12 final size:12
Alignment explanation
Indices: 54514884--54514909 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
54514874 TAAAAATATT
54514884 TAAAATATAATA
1 TAAAATATAATA
54514896 TAAAATATAATA
1 TAAAATATAATA
54514908 TA
1 TA
54514910 TTTAATATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (12 bp):
TAAAATATAATA
Found at i:54515636 original size:14 final size:14
Alignment explanation
Indices: 54515617--54515652 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
54515607 AAAAAGTAAG
54515617 TCATTTTCCAGAAA
1 TCATTTTCCAGAAA
*
54515631 TCATTTTCCGGAAA
1 TCATTTTCCAGAAA
*
54515645 CCATTTTC
1 TCATTTTC
54515653 AGTGAAACAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.28, C:0.25, G:0.08, T:0.39
Consensus pattern (14 bp):
TCATTTTCCAGAAA
Found at i:54518656 original size:21 final size:21
Alignment explanation
Indices: 54518632--54518680 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
54518622 CTTAAAGCTT
54518632 TTTTTTTAATTGACAAATATA
1 TTTTTTTAATTGACAAATATA
*
54518653 TTTTTTTAATTGATAAATATA
1 TTTTTTTAATTGACAAATATA
*
54518674 TTATTTT
1 TTTTTTT
54518681 CAAGTTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.59
Consensus pattern (21 bp):
TTTTTTTAATTGACAAATATA
Found at i:54519164 original size:21 final size:22
Alignment explanation
Indices: 54519121--54519164 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
54519111 TTATTTGATT
* * *
54519121 TTAAAAATACAAGAGTTATTAA
1 TTAAAAATACAAAACTTAATAA
54519143 TTAAAAATA-AAAACTTAATAA
1 TTAAAAATACAAAACTTAATAA
54519164 T
1 T
54519165 ATATTTATTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.59, C:0.05, G:0.05, T:0.32
Consensus pattern (22 bp):
TTAAAAATACAAAACTTAATAA
Found at i:54519337 original size:3 final size:3
Alignment explanation
Indices: 54519329--54519363 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
54519319 ATTAATTAAA
*
54519329 AAT AAT AAT AAT AAC AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
54519364 AACTTGAAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:54519839 original size:19 final size:19
Alignment explanation
Indices: 54519789--54519841 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 19
54519779 TGGATTTAAA
* *
54519789 AGATTATTTCTATAATTTTT
1 AGATTATTTATAT-ATATTT
* * *
54519809 AGAGTCTATATATATATTT
1 AGATTATTTATATATATTT
54519828 AGATTATTTATATA
1 AGATTATTTATATA
54519842 CTTTTCTGTT
Statistics
Matches: 25, Mismatches: 8, Indels: 1
0.74 0.24 0.03
Matches are distributed among these distances:
19 16 0.64
20 9 0.36
ACGTcount: A:0.36, C:0.04, G:0.08, T:0.53
Consensus pattern (19 bp):
AGATTATTTATATATATTT
Found at i:54528901 original size:6 final size:6
Alignment explanation
Indices: 54528890--54528931 Score: 57
Period size: 6 Copynumber: 7.0 Consensus size: 6
54528880 TGGATGAACA
* * *
54528890 TCTGAT TCTGAT TCTGAT TCTAAT GCTGAT TCTGGT TCTGAT
1 TCTGAT TCTGAT TCTGAT TCTGAT TCTGAT TCTGAT TCTGAT
54528932 GTAGATGTTA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.17, C:0.17, G:0.19, T:0.48
Consensus pattern (6 bp):
TCTGAT
Found at i:54535260 original size:16 final size:16
Alignment explanation
Indices: 54535239--54535278 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
54535229 CCTACTCCCT
54535239 CCCAATTTAAACCCAG
1 CCCAATTTAAACCCAG
*
54535255 CCCAATTTAAATCCAG
1 CCCAATTTAAACCCAG
54535271 CCCAATTT
1 CCCAATTT
54535279 TCTCTTAGGC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.35, C:0.35, G:0.05, T:0.25
Consensus pattern (16 bp):
CCCAATTTAAACCCAG
Found at i:54536013 original size:9 final size:9
Alignment explanation
Indices: 54535999--54536071 Score: 74
Period size: 9 Copynumber: 7.7 Consensus size: 9
54535989 CCTAATTTTT
54535999 TAATTTGGG
1 TAATTTGGG
**
54536008 TAATTTGAA
1 TAATTTGGG
54536017 TAATTTTCGGG
1 TAA-TTT-GGG
54536028 TAATTTGGG
1 TAATTTGGG
54536037 TAATTTTCGGG
1 TAA-TTT-GGG
*
54536048 TAATTCGGG
1 TAATTTGGG
*
54536057 TAATTCGGG
1 TAATTTGGG
54536066 TAATTT
1 TAATTT
54536072 TTAACCAAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
9 33 0.61
10 11 0.20
11 10 0.19
ACGTcount: A:0.25, C:0.05, G:0.26, T:0.44
Consensus pattern (9 bp):
TAATTTGGG
Found at i:54536030 original size:20 final size:20
Alignment explanation
Indices: 54536005--54536052 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
54535995 TTTTTAATTT
54536005 GGGTAATTTGAATAATTTTC
1 GGGTAATTTGAATAATTTTC
**
54536025 GGGTAATTTGGGTAATTTTC
1 GGGTAATTTGAATAATTTTC
54536045 GGGTAATT
1 GGGTAATT
54536053 CGGGTAATTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.25, C:0.04, G:0.27, T:0.44
Consensus pattern (20 bp):
GGGTAATTTGAATAATTTTC
Found at i:54536057 original size:20 final size:20
Alignment explanation
Indices: 54536017--54536070 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
54536007 GTAATTTGAA
*
54536017 TAATTTTCGGGTAATTTGGG
1 TAATTTTCGGGTAATTCGGG
54536037 TAATTTTCGGGTAATTCGGG
1 TAATTTTCGGGTAATTCGGG
54536057 TAA--TTCGGGTAATT
1 TAATTTTCGGGTAATT
54536071 TTTAACCAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
18 11 0.33
20 22 0.67
ACGTcount: A:0.22, C:0.07, G:0.28, T:0.43
Consensus pattern (20 bp):
TAATTTTCGGGTAATTCGGG
Found at i:54536434 original size:24 final size:24
Alignment explanation
Indices: 54536407--54536470 Score: 60
Period size: 26 Copynumber: 2.6 Consensus size: 24
54536397 AATAAAACTT
54536407 ATTAAAAATAT-AAGAA-ATATATAA
1 ATTAAAAAT-TCAA-AATATATATAA
54536431 ATTATAAAACTTCAAAATATATATAA
1 ATTA-AAAA-TTCAAAATATATATAA
* *
54536457 ATTGAAAATGCAAA
1 ATTAAAAATTCAAA
54536471 TAAAAAAGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
24 9 0.26
25 11 0.32
26 14 0.41
ACGTcount: A:0.61, C:0.05, G:0.05, T:0.30
Consensus pattern (24 bp):
ATTAAAAATTCAAAATATATATAA
Found at i:54538011 original size:19 final size:17
Alignment explanation
Indices: 54537979--54538013 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
54537969 ATCGTTCTTG
54537979 ATTTTCTTTTTCTAATT
1 ATTTTCTTTTTCTAATT
54537996 ATTTTCATTATTTCTAAT
1 ATTTTC-TT-TTTCTAAT
54538014 CTGTATTGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 2 0.12
19 8 0.50
ACGTcount: A:0.23, C:0.11, G:0.00, T:0.66
Consensus pattern (17 bp):
ATTTTCTTTTTCTAATT
Found at i:54539873 original size:18 final size:18
Alignment explanation
Indices: 54539847--54539899 Score: 63
Period size: 17 Copynumber: 2.8 Consensus size: 18
54539837 AAAATTCAGA
54539847 AAAATATAAAAATTATTTT
1 AAAA-ATAAAAATTATTTT
*
54539866 AAAAAT-AAAATTAATTT
1 AAAAATAAAAATTATTTT
54539883 AAAAATTATAAAATTAT
1 AAAAA-TA-AAAATTAT
54539900 AAAAAATATT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
17 15 0.52
18 3 0.10
19 4 0.14
20 7 0.24
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
AAAAATAAAAATTATTTT
Found at i:54544396 original size:43 final size:43
Alignment explanation
Indices: 54544334--54544629 Score: 319
Period size: 43 Copynumber: 6.9 Consensus size: 43
54544324 TTTTTCACAT
* * *
54544334 AAACGCCGCTGAAGGTCATGACCTTAAGCGGCGCTTTTATCAC
1 AAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTTATCAC
* * *
54544377 AAACGCCGCTATAGATCATGACCTTTAGTGGCGCTTTTGT-ATC
1 AAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTTATCA-C
* * **
54544420 AAACGCCACTAAAGGTCATGTTCTTTAGCGGCGCTTTTATCAC
1 AAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTTATCAC
*
54544463 AAACGCCGCTATAGATCATGACCTTTAGCGGCGCTTTTAT-AGC
1 AAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTTATCA-C
* * * *** * *
54544506 AATCGCCGCTAAAGGTAATGTTGTTTAGCGGCGCTTTCATTAC
1 AAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTTATCAC
* * * **
54544549 AAACGCCACTAAAGAACATGACCTTTAGCGACGCTTTTATCGT
1 AAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTTATCAC
* *
54544592 AAACGCTGCTAAAGAACATGACCTTTAGCGGCG-TTTTA
1 AAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTTA
54544630 CTAAAAACGC
Statistics
Matches: 207, Mismatches: 42, Indels: 9
0.80 0.16 0.03
Matches are distributed among these distances:
42 7 0.03
43 198 0.96
44 2 0.01
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.28
Consensus pattern (43 bp):
AAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTTATCAC
Found at i:54544439 original size:86 final size:85
Alignment explanation
Indices: 54544334--54544629 Score: 353
Period size: 86 Copynumber: 3.5 Consensus size: 85
54544324 TTTTTCACAT
* *
54544334 AAACGCCGCTGAAGGTCATGACCTTAAGCGGCGCTTTTATCACAAACGCCGCTATAGATCATGAC
1 AAACGCCGCTAAAGGTCATGACCTTTAGCGGCGCTTTTATCACAAACGCCGCTATAGATCATGAC
*
54544399 CTTTAGTGGCGCTTTTGTATC
66 CTTTAGCGGCGCTTTT-TATC
* **
54544420 AAACGCCACTAAAGGTCATGTTCTTTAGCGGCGCTTTTATCACAAACGCCGCTATAGATCATGAC
1 AAACGCCGCTAAAGGTCATGACCTTTAGCGGCGCTTTTATCACAAACGCCGCTATAGATCATGAC
*
54544485 CTTTAGCGGCGCTTTTATAGC
66 CTTTAGCGGCGCTTTT-TATC
* * *** * * * * *
54544506 AATCGCCGCTAAAGGTAATGTTGTTTAGCGGCGCTTTCATTACAAACGCCACTAAAGAACATGAC
1 AAACGCCGCTAAAGGTCATGACCTTTAGCGGCGCTTTTATCACAAACGCCGCTATAGATCATGAC
*
54544571 CTTTAGCGACGC-TTTTATC
66 CTTTAGCGGCGCTTTTTATC
* **
54544590 GTAAACGCTGCTAAAGAACATGACCTTTAGCGGCG-TTTTA
1 --AAACGCCGCTAAAGGTCATGACCTTTAGCGGCGCTTTTA
54544630 CTAAAAACGC
Statistics
Matches: 180, Mismatches: 28, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
84 3 0.02
85 7 0.04
86 170 0.94
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.28
Consensus pattern (85 bp):
AAACGCCGCTAAAGGTCATGACCTTTAGCGGCGCTTTTATCACAAACGCCGCTATAGATCATGAC
CTTTAGCGGCGCTTTTTATC
Found at i:54544947 original size:21 final size:21
Alignment explanation
Indices: 54544922--54544978 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
54544912 ATCGTATTTT
*
54544922 CTGCTGCCTTTGCTTCCCTCG
1 CTGCTGCCTCTGCTTCCCTCG
*
54544943 TTGCTGCCTCTGCTTCCCTCG
1 CTGCTGCCTCTGCTTCCCTCG
54544964 CTGCTGCCTCTGCTT
1 CTGCTGCCTCTGCTT
54544979 TAAGTTGTAG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.00, C:0.42, G:0.19, T:0.39
Consensus pattern (21 bp):
CTGCTGCCTCTGCTTCCCTCG
Found at i:54549314 original size:366 final size:366
Alignment explanation
Indices: 54548642--54549376 Score: 1470
Period size: 366 Copynumber: 2.0 Consensus size: 366
54548632 GCATGACATT
54548642 AAGATTGTGTTGTAAAATGTGATGCTCCCAATAAGGCAACTCAAATAAAATACTTCTTTTTTTTC
1 AAGATTGTGTTGTAAAATGTGATGCTCCCAATAAGGCAACTCAAATAAAATACTTCTTTTTTTTC
54548707 CACAAGTCTGCCTCATTATGATCATCCTCTTCATCAAATTCATCATTTGATCTTCTAATTCTTTG
66 CACAAGTCTGCCTCATTATGATCATCCTCTTCATCAAATTCATCATTTGATCTTCTAATTCTTTG
54548772 CGTGTTGGGCGGTTGATTCATTTTCCCATAACTGAAATTCATATCTTTCAACATGAACAAGATTT
131 CGTGTTGGGCGGTTGATTCATTTTCCCATAACTGAAATTCATATCTTTCAACATGAACAAGATTT
54548837 CAGATCCACCGGTGTATGAAGGAGCTTCTCTGAATTCTTCAGTGTCGTCAAATAGAGTACTCTGA
196 CAGATCCACCGGTGTATGAAGGAGCTTCTCTGAATTCTTCAGTGTCGTCAAATAGAGTACTCTGA
54548902 AATCTAAATTTATGATTTCCCCGTAACCACCGACGATGCCCCATGTAAGAGAACTTCTTCCCGTT
261 AATCTAAATTTATGATTTCCCCGTAACCACCGACGATGCCCCATGTAAGAGAACTTCTTCCCGTT
54548967 GTATAAACATTGCGAACATGTTTGCGCAGCACAACAAGGAC
326 GTATAAACATTGCGAACATGTTTGCGCAGCACAACAAGGAC
54549008 AAGATTGTGTTGTAAAATGTGATGCTCCCAATAAGGCAACTCAAATAAAATACTTCTTTTTTTTC
1 AAGATTGTGTTGTAAAATGTGATGCTCCCAATAAGGCAACTCAAATAAAATACTTCTTTTTTTTC
54549073 CACAAGTCTGCCTCATTATGATCATCCTCTTCATCAAATTCATCATTTGATCTTCTAATTCTTTG
66 CACAAGTCTGCCTCATTATGATCATCCTCTTCATCAAATTCATCATTTGATCTTCTAATTCTTTG
54549138 CGTGTTGGGCGGTTGATTCATTTTCCCATAACTGAAATTCATATCTTTCAACATGAACAAGATTT
131 CGTGTTGGGCGGTTGATTCATTTTCCCATAACTGAAATTCATATCTTTCAACATGAACAAGATTT
54549203 CAGATCCACCGGTGTATGAAGGAGCTTCTCTGAATTCTTCAGTGTCGTCAAATAGAGTACTCTGA
196 CAGATCCACCGGTGTATGAAGGAGCTTCTCTGAATTCTTCAGTGTCGTCAAATAGAGTACTCTGA
54549268 AATCTAAATTTATGATTTCCCCGTAACCACCGACGATGCCCCATGTAAGAGAACTTCTTCCCGTT
261 AATCTAAATTTATGATTTCCCCGTAACCACCGACGATGCCCCATGTAAGAGAACTTCTTCCCGTT
54549333 GTATAAACATTGCGAACATGTTTGCGCAGCACAACAAGGAC
326 GTATAAACATTGCGAACATGTTTGCGCAGCACAACAAGGAC
54549374 AAG
1 AAG
54549377 CATAACGTCC
Statistics
Matches: 369, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
366 369 1.00
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (366 bp):
AAGATTGTGTTGTAAAATGTGATGCTCCCAATAAGGCAACTCAAATAAAATACTTCTTTTTTTTC
CACAAGTCTGCCTCATTATGATCATCCTCTTCATCAAATTCATCATTTGATCTTCTAATTCTTTG
CGTGTTGGGCGGTTGATTCATTTTCCCATAACTGAAATTCATATCTTTCAACATGAACAAGATTT
CAGATCCACCGGTGTATGAAGGAGCTTCTCTGAATTCTTCAGTGTCGTCAAATAGAGTACTCTGA
AATCTAAATTTATGATTTCCCCGTAACCACCGACGATGCCCCATGTAAGAGAACTTCTTCCCGTT
GTATAAACATTGCGAACATGTTTGCGCAGCACAACAAGGAC
Found at i:54550849 original size:9 final size:9
Alignment explanation
Indices: 54550835--54551242 Score: 131
Period size: 9 Copynumber: 43.9 Consensus size: 9
54550825 TAAGTATAAT
54550835 TAAGTTATG
1 TAAGTTATG
54550844 TAAGTTATG
1 TAAGTTATG
* *
54550853 ATATGATATATA
1 -TAAG-T-TATG
54550865 TAAGTTAT-
1 TAAGTTATG
*
54550873 TAAGCTATG
1 TAAGTTATG
54550882 TAAGTTATG
1 TAAGTTATG
*
54550891 TGAGTTATG
1 TAAGTTATG
* *
54550900 ATATGATATATA
1 -TAAG-T-TATG
*
54550912 TAATTTAT-
1 TAAGTTATG
54550920 TAAGTTATG
1 TAAGTTATG
*
54550929 TATG-TATG
1 TAAGTTATG
*
54550937 TGAGTTATG
1 TAAGTTATG
54550946 TAAGTTATG
1 TAAGTTATG
* * *
54550955 ATATGATATA
1 -TAAGTTATG
*
54550965 T-ATTTATG
1 TAAGTTATG
54550973 T-A-TTATG
1 TAAGTTATG
54550980 TAAGTTATGTG
1 TAAGTTA--TG
** *
54550991 TTTGTTTTG
1 TAAGTTATG
54551000 TAAGTTATGG
1 TAAGTTAT-G
* *
54551010 TATGATATATA
1 TAAG-T-TATG
54551021 TAAGTTAT-
1 TAAGTTATG
54551029 TAAGTTATG
1 TAAGTTATG
*
54551038 TATG-TATG
1 TAAGTTATG
*
54551046 TGAGTTATG
1 TAAGTTATG
54551055 TAAGTTATG
1 TAAGTTATG
*
54551064 ATCTAA-TATATA
1 ---TAAGT-TATG
54551076 TAAGTTAT-
1 TAAGTTATG
*
54551084 TAAGTTAAG
1 TAAGTTATG
* *
54551093 ATCCAAAGTTTTTTT
1 -T---AAG--TTATG
* *
54551108 TAA-TTCTT
1 TAAGTTATG
54551116 TAAAGTTATG
1 T-AAGTTATG
*
54551126 TAAATTATG
1 TAAGTTATG
54551135 TAAGTTATG
1 TAAGTTATG
*
54551144 ATATGGTTAT-
1 -TA-AGTTATG
54551154 TAAGTTATG
1 TAAGTTATG
*
54551163 CAAGTTATG
1 TAAGTTATG
*
54551172 TGAGTTATG
1 TAAGTTATG
* *
54551181 TAAATTATA
1 TAAGTTATG
*
54551190 TAAATTATG
1 TAAGTTATG
* *
54551199 TAAATTTTG
1 TAAGTTATG
* * *
54551208 ATATGATATA
1 -TAAGTTATG
*
54551218 T-ATTTATG
1 TAAGTTATG
54551226 TAAGTTATG
1 TAAGTTATG
*
54551235 TAAATTAT
1 TAAGTTAT
54551243 ATATTCATTT
Statistics
Matches: 294, Mismatches: 67, Indels: 76
0.67 0.15 0.17
Matches are distributed among these distances:
7 6 0.02
8 61 0.21
9 151 0.51
10 30 0.10
11 25 0.09
12 15 0.05
13 3 0.01
14 1 0.00
15 2 0.01
ACGTcount: A:0.35, C:0.01, G:0.17, T:0.47
Consensus pattern (9 bp):
TAAGTTATG
Found at i:54550927 original size:55 final size:55
Alignment explanation
Indices: 54550865--54551090 Score: 275
Period size: 55 Copynumber: 4.1 Consensus size: 55
54550855 ATGATATATA
* * *
54550865 TAAGTTAT-TAAGCTATGTAAGTTATGTGAGTTATGATATGATATATATAATTTAT
1 TAAGTTATGTAAG-TATGTGAGTTATGTAAGTTATGATATGATATATATAAGTTAT
*
54550920 TAAGTTATGTATGTATGTGAGTTATGTAAGTTATGATATGATATATAT---TTAT
1 TAAGTTATGTAAGTATGTGAGTTATGTAAGTTATGATATGATATATATAAGTTAT
* * *
54550972 GT-A-TTATGTAAGTTATGTGTTTGTTTTGTAAGTTATGGTATGATATATATAAGTTAT
1 -TAAGTTATGTAAG-TATGTG--AGTTATGTAAGTTATGATATGATATATATAAGTTAT
* * *
54551029 TAAGTTATGTATGTATGTGAGTTATGTAAGTTATGATCTAATATATATAAGTTAT
1 TAAGTTATGTAAGTATGTGAGTTATGTAAGTTATGATATGATATATATAAGTTAT
54551084 TAAGTTA
1 TAAGTTA
54551091 AGATCCAAAG
Statistics
Matches: 148, Mismatches: 13, Indels: 20
0.82 0.07 0.11
Matches are distributed among these distances:
51 8 0.05
52 11 0.07
53 1 0.01
54 26 0.18
55 79 0.53
56 4 0.03
57 11 0.07
58 8 0.05
ACGTcount: A:0.33, C:0.01, G:0.19, T:0.47
Consensus pattern (55 bp):
TAAGTTATGTAAGTATGTGAGTTATGTAAGTTATGATATGATATATATAAGTTAT
Found at i:54551032 original size:109 final size:103
Alignment explanation
Indices: 54550837--54551087 Score: 344
Period size: 109 Copynumber: 2.4 Consensus size: 103
54550827 AGTATAATTA
*
54550837 AGTTATGTAAGTTATGATATGATATATA-TAAGTTATTAAGCTATGTAAGTTATGTGAGTTATGA
1 AGTTATGTAAGTTATGATATGATATATATTAAGTTATTAAGCTATGTAAGTTATGTAAGTTATGA
*
54550901 TATGATATATATAATTTATTAAGTTATGTATGTATGTG
66 TATGATATATATAAGTTATTAAGTTATGTATGTATGTG
* * ** *
54550939 AGTTATGTAAGTTATGATATGATATATATTTATGTATTATGTAAGTTATGTGTTTGTTTTGTAAG
1 AGTTATGTAAGTTATGATATGATATATA-TTAAG--TTAT-TAAGCTA--TGTAAGTTATGTAAG
*
54551004 TTATGGTATGATATATATAAGTTATTAAGTTATGTATGTATGTG
60 TTATGATATGATATATATAAGTTATTAAGTTATGTATGTATGTG
* *
54551048 AGTTATGTAAGTTATGATCTAATATATA-TAAGTTATTAAG
1 AGTTATGTAAGTTATGATATGATATATATTAAGTTATTAAG
54551088 TTAAGATCCA
Statistics
Matches: 131, Mismatches: 11, Indels: 12
0.85 0.07 0.08
Matches are distributed among these distances:
102 28 0.21
104 7 0.05
105 4 0.03
106 4 0.03
107 9 0.07
109 79 0.60
ACGTcount: A:0.34, C:0.01, G:0.19, T:0.47
Consensus pattern (103 bp):
AGTTATGTAAGTTATGATATGATATATATTAAGTTATTAAGCTATGTAAGTTATGTAAGTTATGA
TATGATATATATAAGTTATTAAGTTATGTATGTATGTG
Found at i:54552843 original size:64 final size:63
Alignment explanation
Indices: 54552753--54552913 Score: 162
Period size: 64 Copynumber: 2.5 Consensus size: 63
54552743 AACATATGAG
* * * * * *
54552753 CCACATGGGTAAGGGACACGGGCGTGTGTCCAGGCCATGTAACTTATTGATTAAAAGA-TAAGGA
1 CCACACGGGTCAGGGACACAGACGTGTGTCCAGGCCACGTAACTTACTG-TT-AAAGATTAAGGA
* * * *** *
54552817 TCACACGGGTCAGGGACACAGACGTGTGTCCAGGCCGCGTGACTTACTGTTTGTGATTTAGGA
1 CCACACGGGTCAGGGACACAGACGTGTGTCCAGGCCACGTAACTTACTGTTAAAGATTAAGGA
* *
54552880 CCACACGAGTCAGAGACACAGACGTGTGTCCAGG
1 CCACACGGGTCAGGGACACAGACGTGTGTCCAGG
54552914 TCGTGTGACT
Statistics
Matches: 80, Mismatches: 16, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
62 2 0.03
63 38 0.47
64 40 0.50
ACGTcount: A:0.27, C:0.22, G:0.30, T:0.21
Consensus pattern (63 bp):
CCACACGGGTCAGGGACACAGACGTGTGTCCAGGCCACGTAACTTACTGTTAAAGATTAAGGA
Found at i:54552901 original size:63 final size:63
Alignment explanation
Indices: 54552813--54552949 Score: 184
Period size: 63 Copynumber: 2.2 Consensus size: 63
54552803 TTAAAAGATA
* * * * * *
54552813 AGGATCACACGGGTCAGGGACACAGACGTGTGTCCAGGCCGCGTGACTTACTGTTTGTGATTT
1 AGGACCACACGAGTCAGAGACACAGACGTGTGTCCAGGCCGCGTGACTCACTATTTATGATTT
* * *
54552876 AGGACCACACGAGTCAGAGACACAGACGTGTGTCCAGGTCGTGTGACTCATTATTTATGATTT
1 AGGACCACACGAGTCAGAGACACAGACGTGTGTCCAGGCCGCGTGACTCACTATTTATGATTT
*
54552939 AGGACCTCACG
1 AGGACCACACG
54552950 GGCAAACGAC
Statistics
Matches: 64, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
63 64 1.00
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (63 bp):
AGGACCACACGAGTCAGAGACACAGACGTGTGTCCAGGCCGCGTGACTCACTATTTATGATTT
Found at i:54555846 original size:19 final size:19
Alignment explanation
Indices: 54555808--54555862 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 19
54555798 TATGTTCAAT
*
54555808 GTTTATATATAATTTTTAGA
1 GTTTATATAT-ATATTTAGA
54555828 GTTTATATATATATTTAGA
1 GTTTATATATATATTTAGA
* *
54555847 TTTTTTATATATATTT
1 GTTTATATATATATTT
54555863 CATTATTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 22 0.69
20 10 0.31
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (19 bp):
GTTTATATATATATTTAGA
Found at i:54555871 original size:19 final size:19
Alignment explanation
Indices: 54555833--54555880 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
54555823 TTAGAGTTTA
*
54555833 TATATATATTTAGATTTTT
1 TATATATATTTACATTTTT
54555852 TATATATATTT-CATTATTT
1 TATATATATTTACATT-TTT
*
54555871 T-TATTTATTT
1 TATATATATTT
54555881 TTAATATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 11 0.42
19 15 0.58
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (19 bp):
TATATATATTTACATTTTT
Found at i:54555962 original size:19 final size:18
Alignment explanation
Indices: 54555938--54555985 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
54555928 AAATTATGTA
* *
54555938 TATATATTTCTTTATTTTT
1 TATATAATT-TTTATATTT
54555957 TATATAATTTTTATATTT
1 TATATAATTTTTATATTT
*
54555975 TA-ACAATTTTT
1 TATATAATTTTT
54555986 TAAAGTTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
17 8 0.31
18 10 0.38
19 8 0.31
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (18 bp):
TATATAATTTTTATATTT
Found at i:54559954 original size:21 final size:21
Alignment explanation
Indices: 54559928--54559968 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
54559918 ATCTGCTCAA
* *
54559928 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
54559949 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
54559969 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:54567343 original size:13 final size:13
Alignment explanation
Indices: 54567333--54567362 Score: 51
Period size: 13 Copynumber: 2.2 Consensus size: 13
54567323 TTCTTTTTAT
54567333 TTTTCCTTTTTTC
1 TTTTCCTTTTTTC
54567346 TTTTCCTTTTTTGC
1 TTTTCCTTTTTT-C
54567360 TTT
1 TTT
54567363 ATTATCTCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.00, C:0.20, G:0.03, T:0.77
Consensus pattern (13 bp):
TTTTCCTTTTTTC
Found at i:54569570 original size:25 final size:25
Alignment explanation
Indices: 54569536--54569585 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
54569526 TGGCTTGTGC
*
54569536 TGCAGCATGCTGGCTCA-CTTCATCA
1 TGCAGCATGCTAGC-CATCTTCATCA
54569561 TGCAGCATGCTAGCCATCTTCATCA
1 TGCAGCATGCTAGCCATCTTCATCA
54569586 CTCCTCCTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 2 0.09
25 21 0.91
ACGTcount: A:0.22, C:0.32, G:0.18, T:0.28
Consensus pattern (25 bp):
TGCAGCATGCTAGCCATCTTCATCA
Found at i:54574080 original size:25 final size:25
Alignment explanation
Indices: 54574035--54574084 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
54574025 TGGCTTGTGC
*
54574035 TGCAGCATGCTGGCTCACTTCATCA
1 TGCAGCATGCTAGCTCACTTCATCA
*
54574060 TGCAGCATTCTAGC-CATCTTCATCA
1 TGCAGCATGCTAGCTCA-CTTCATCA
54574085 ATAATATGCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 2 0.09
25 20 0.91
ACGTcount: A:0.22, C:0.32, G:0.16, T:0.30
Consensus pattern (25 bp):
TGCAGCATGCTAGCTCACTTCATCA
Found at i:54575756 original size:17 final size:16
Alignment explanation
Indices: 54575731--54575776 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 16
54575721 AAAATACAGT
54575731 CCGTATTTTTAGAAAA
1 CCGTATTTTTAGAAAA
* * *
54575747 CCTTTATTTTCATAAAA
1 CC-GTATTTTTAGAAAA
54575764 CCGTATTTTTAGA
1 CCGTATTTTTAGA
54575777 CACGCATTAC
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
16 10 0.43
17 13 0.57
ACGTcount: A:0.33, C:0.15, G:0.09, T:0.43
Consensus pattern (16 bp):
CCGTATTTTTAGAAAA
Found at i:54576642 original size:32 final size:32
Alignment explanation
Indices: 54576567--54576643 Score: 84
Period size: 33 Copynumber: 2.3 Consensus size: 32
54576557 CGTGTGGCTT
*
54576567 GCCCGTGTGGGCCCACACACCCAGATTAGCCTT
1 GCCCGTGT-GGCCCACACACCCAGATTAGCCTA
* * *
54576600 GCCCCGTGTGGCCCACACCCCCA-ACTTGGTCTA
1 G-CCCGTGTGGCCCACACACCCAGA-TTAGCCTA
54576633 GCCCGTGTGGC
1 GCCCGTGTGGC
54576644 TTACACGACC
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
32 11 0.29
33 20 0.53
34 7 0.18
ACGTcount: A:0.14, C:0.42, G:0.26, T:0.18
Consensus pattern (32 bp):
GCCCGTGTGGCCCACACACCCAGATTAGCCTA
Found at i:54582368 original size:11 final size:11
Alignment explanation
Indices: 54582354--54582380 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
54582344 TGTTTTCCTT
54582354 TATTTTTTATA
1 TATTTTTTATA
54582365 TATTTTTTATA
1 TATTTTTTATA
54582376 TATTT
1 TATTT
54582381 ACAATTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (11 bp):
TATTTTTTATA
Found at i:54587328 original size:11 final size:11
Alignment explanation
Indices: 54587308--54587415 Score: 58
Period size: 11 Copynumber: 10.4 Consensus size: 11
54587298 ACAAAAATTA
54587308 AAAAAGTATTTT
1 AAAAA-TATTTT
54587320 AAAAATATTTT
1 AAAAATATTTT
54587331 --AAA-A--TT
1 AAAAATATTTT
* *
54587337 AAAAA-AATTA
1 AAAAATATTTT
54587347 AAAAAGTATTTT
1 AAAAA-TATTTT
54587359 AAAAATATTTT
1 AAAAATATTTT
54587370 --AAA-A--TT
1 AAAAATATTTT
*
54587376 AAAAAAATTTT
1 AAAAATATTTT
54587387 AAAAAAAGTATTTT
1 --AAAAA-TATTTT
*
54587401 AAAAGTATTTT
1 AAAAATATTTT
54587412 AAAA
1 AAAA
54587416 TTAAAAAATA
Statistics
Matches: 77, Mismatches: 5, Indels: 29
0.69 0.05 0.26
Matches are distributed among these distances:
6 4 0.05
8 9 0.12
9 7 0.09
10 6 0.08
11 24 0.31
12 17 0.22
13 5 0.06
14 5 0.06
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:54587393 original size:30 final size:30
Alignment explanation
Indices: 54587340--54587404 Score: 89
Period size: 30 Copynumber: 2.1 Consensus size: 30
54587330 TAAAATTAAA
54587340 AAAATTAAAAAAGTATTTTAAAAA-TATTTT
1 AAAATTAAAAAAG-ATTTTAAAAAGTATTTT
54587370 AAAATTAAAAAA-ATTTTAAAAAAAGTATTTT
1 AAAATTAAAAAAGATTTT--AAAAAGTATTTT
54587401 AAAA
1 AAAA
54587405 GTATTTTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
28 5 0.16
30 17 0.53
31 10 0.31
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (30 bp):
AAAATTAAAAAAGATTTTAAAAAGTATTTT
Found at i:54587393 original size:81 final size:81
Alignment explanation
Indices: 54587282--54587431 Score: 232
Period size: 81 Copynumber: 1.9 Consensus size: 81
54587272 ACCAAAATTT
*
54587282 TATTTTAAAAATTAAAACAAAAATTAAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAATTA
1 TATTTTAAAAATTAAAACAAAAATTAAAAAAGTATTTTAAAAATATTTTAAAATT-AAAAAATAA
54587347 AAAAAGTATTTTAAAAA
65 AAAAAGTATTTTAAAAA
** *
54587364 TATTTT-AAAATTAAAA-AAATTTTAAAAAAAGTATTTTAAAAGTATTTTAAAATTAAAAAATAA
1 TATTTTAAAAATTAAAACAAAAATT-AAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAATAA
54587427 AAAAA
65 AAAAA
54587432 TAAAAATATT
Statistics
Matches: 63, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
80 18 0.29
81 39 0.62
82 6 0.10
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.35
Consensus pattern (81 bp):
TATTTTAAAAATTAAAACAAAAATTAAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAATAAA
AAAAGTATTTTAAAAA
Found at i:54590760 original size:19 final size:19
Alignment explanation
Indices: 54590738--54590784 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
54590728 TCAAAGGTTA
* *
54590738 TATATATATTTTGATTATT
1 TATATATATTTTCATAATT
54590757 TATATACT-TTTTCATAATT
1 TATATA-TATTTTCATAATT
*
54590776 TTTATATAT
1 TATATATAT
54590785 ATATTTCAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
18 1 0.04
19 21 0.91
20 1 0.04
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (19 bp):
TATATATATTTTCATAATT
Found at i:54590859 original size:30 final size:30
Alignment explanation
Indices: 54590806--54590863 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
54590796 TCCTTTCTAT
54590806 TTTATATTTTTAAATTATGTATATATTTTTC
1 TTTATATTTTTAAATTATGTATAT-TTTTTC
* * *
54590837 TTTAT-TTTTTACATTTTTTATATTTTT
1 TTTATATTTTTAAATTATGTATATTTTT
54590864 AAAATTTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 4 0.17
30 15 0.62
31 5 0.21
ACGTcount: A:0.24, C:0.03, G:0.02, T:0.71
Consensus pattern (30 bp):
TTTATATTTTTAAATTATGTATATTTTTTC
Found at i:54592404 original size:2 final size:2
Alignment explanation
Indices: 54592399--54592433 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
54592389 TAGGCATGTT
54592399 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
54592434 TTTCTATTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:54592591 original size:13 final size:12
Alignment explanation
Indices: 54592573--54592602 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
54592563 TTTCATAGTT
54592573 TATTTATATATTA
1 TATTTATATA-TA
54592586 TATTTATATATA
1 TATTTATATATA
54592598 TATTT
1 TATTT
54592603 TGTTCTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.41
13 10 0.59
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (12 bp):
TATTTATATATA
Found at i:54595084 original size:41 final size:40
Alignment explanation
Indices: 54595030--54595222 Score: 223
Period size: 41 Copynumber: 4.9 Consensus size: 40
54595020 GACCTTTTCG
*
54595030 GGGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTC
1 GGGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
* * *
54595070 GGGGCTTTAGCGGCGTTTTTGAGAAAGTGCCGCTAATACT-
1 -GGGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
* * *
54595110 --TCTTTAGCAGCATTTTTGAAAAAGCGCCGCTAATGCTC
1 GGGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
* * * *
54595148 TAGTCTTTAGCGGAGTTTTTGAAAAAGCACCGCTAATGCT-
1 -GGGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
* *
54595188 GGGCTTTAGCGGCGTTTTTAAAAAAGCGCCACTAA
1 GGGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAA
54595223 AACATTTTAT
Statistics
Matches: 130, Mismatches: 18, Indels: 10
0.82 0.11 0.06
Matches are distributed among these distances:
37 31 0.24
39 29 0.22
41 70 0.54
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.30
Consensus pattern (40 bp):
GGGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
Found at i:54595134 original size:78 final size:79
Alignment explanation
Indices: 54595031--54595222 Score: 242
Period size: 78 Copynumber: 2.4 Consensus size: 79
54595021 ACCTTTTCGG
* * * *
54595031 GGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCGGGGCTTTAGCGGCGTTTTTGAGAAA
1 GGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCGAGGCTTTAGCGGAGTTTTTGAAAAA
**
54595096 GTGCCGCTAATACT
66 GCACCGCTAATACT
* * * * *
54595110 -TCTTTAGCAGCATTTTTGAAAAAGCGCCGCTAATGCTCTAGTCTTTAGCGGAGTTTTTGAAAAA
1 GGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCGAGGCTTTAGCGGAGTTTTTGAAAAA
*
54595174 GCACCGCTAATGCT
66 GCACCGCTAATACT
* *
54595188 GGGCTTTAGCGGCGTTTTTAAAAAAGCGCCACTAA
1 -GGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAA
54595223 AACATTTTAT
Statistics
Matches: 94, Mismatches: 17, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
78 66 0.70
80 28 0.30
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.30
Consensus pattern (79 bp):
GGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCGAGGCTTTAGCGGAGTTTTTGAAAAA
GCACCGCTAATACT
Found at i:54595615 original size:14 final size:15
Alignment explanation
Indices: 54595598--54595639 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
54595588 TAGGGATTAT
54595598 GGTTTAAGGGTT-GG
1 GGTTTAAGGGTTAGG
*
54595612 GGTTTAAGGTTTAGG
1 GGTTTAAGGGTTAGG
*
54595627 GG-TTAGGGGTTAG
1 GGTTTAAGGGTTAG
54595640 ACATTGTAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 20 0.83
15 4 0.17
ACGTcount: A:0.17, C:0.00, G:0.48, T:0.36
Consensus pattern (15 bp):
GGTTTAAGGGTTAGG
Found at i:54595637 original size:15 final size:15
Alignment explanation
Indices: 54595569--54595639 Score: 51
Period size: 14 Copynumber: 4.9 Consensus size: 15
54595559 ACTGTTTTAA
54595569 GGTTTAGGGAG-TAGG
1 GGTTTAGGG-GTTAGG
* * *
54595584 GATTTAGGGATTA-T
1 GGTTTAGGGGTTAGG
*
54595598 GGTTTAAGGGTT-GG
1 GGTTTAGGGGTTAGG
* *
54595612 GGTTTAAGGTTTAGG
1 GGTTTAGGGGTTAGG
54595627 GG-TTAGGGGTTAG
1 GGTTTAGGGGTTAG
54595640 ACATTGTAGG
Statistics
Matches: 43, Mismatches: 10, Indels: 7
0.72 0.17 0.12
Matches are distributed among these distances:
14 29 0.67
15 14 0.33
ACGTcount: A:0.20, C:0.00, G:0.45, T:0.35
Consensus pattern (15 bp):
GGTTTAGGGGTTAGG
Found at i:54595799 original size:21 final size:21
Alignment explanation
Indices: 54595775--54595814 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
54595765 TATGGTTTGT
* *
54595775 GGTTTATGGTTTAAGGGTTGG
1 GGTTTAAGGTTTAAAGGTTGG
54595796 GGTTTAAGGTTTAAAGGTT
1 GGTTTAAGGTTTAAAGGTT
54595815 AGTGGTTAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.20, C:0.00, G:0.38, T:0.42
Consensus pattern (21 bp):
GGTTTAAGGTTTAAAGGTTGG
Found at i:54599775 original size:43 final size:43
Alignment explanation
Indices: 54599693--54599785 Score: 116
Period size: 43 Copynumber: 2.2 Consensus size: 43
54599683 TCATAAATGC
* *
54599693 CGTTAAAGAAAGGTACTTTTAGCGGTGTTTGTGATAAAAGCGT
1 CGTTAAAGAAAGGTACTTTTAGCGGCGTTTGTGAGAAAAGCGT
* * *
54599736 CGTTAAAGAATGGTACTTTTAGTGGCGTTTAG-GAGAAAAGTGT
1 CGTTAAAGAAAGGTACTTTTAGCGGCGTTT-GTGAGAAAAGCGT
*
54599779 CGCTAAA
1 CGTTAAA
54599786 AGTCATGATT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
43 42 0.98
44 1 0.02
ACGTcount: A:0.31, C:0.10, G:0.28, T:0.31
Consensus pattern (43 bp):
CGTTAAAGAAAGGTACTTTTAGCGGCGTTTGTGAGAAAAGCGT
Found at i:54602351 original size:17 final size:17
Alignment explanation
Indices: 54602331--54602381 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 17
54602321 ATAATCCCAT
54602331 AAAAATTATAAAAATAA
1 AAAAATTATAAAAATAA
* *
54602348 AAAAATTATAAAGATTTCA
1 AAAAATTATAAA-A-ATAA
54602367 AAAAATTA-AAAAATA
1 AAAAATTATAAAAATA
54602382 TTTTAAAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
16 1 0.04
17 13 0.46
18 4 0.14
19 10 0.36
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.25
Consensus pattern (17 bp):
AAAAATTATAAAAATAA
Found at i:54603518 original size:19 final size:19
Alignment explanation
Indices: 54603496--54603533 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
54603486 AAAAAAAGAG
*
54603496 TTTT-TTTTTTAAATATATA
1 TTTTATTTTTCAAAT-TATA
54603515 TTTTATTTTTCAAATTATA
1 TTTTATTTTTCAAATTATA
54603534 AAAAATCTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.66
Consensus pattern (19 bp):
TTTTATTTTTCAAATTATA
Found at i:54607422 original size:144 final size:144
Alignment explanation
Indices: 54606978--54607412 Score: 538
Period size: 144 Copynumber: 3.0 Consensus size: 144
54606968 GATAAGCTGC
* * *
54606978 TCAAGTTTCCTATGGAAGTAGGGATTTGTCCAGAGAATGTGTTATTAGACAGATACAATTGACTA
1 TCAAGTTTCCTATGGAAGTAGGGATTTGTCCAGAGAATGTGTTATTGGACAGATCCAATTCACTA
* * *
54607043 AGAGATTTAAGCATCCCTACCTCTTTAGGTATCAATCCAAAAAACATATTGTCAAAAAGGCTAAG
66 AGAGATTTAAGCATCCCTACCTCTTTAGGTATCAATCCAGAAAACATATTATCAAAAAGGATAAG
54607108 AGTAGTTAAGTTGG
131 AGTAGTTAAGTTGG
* * *
54607122 TCAAGTTTCCTATGGAAGTAGGGATTTGTCCAGAGAATGTGTTACTGGACAGATCCAATTTACTG
1 TCAAGTTTCCTATGGAAGTAGGGATTTGTCCAGAGAATGTGTTATTGGACAGATCCAATTCACTA
* * ** * *
54607187 AGAGATTTAAGCATCCCTACCTCTTTAGGGATGACGCCACTG-AGA-TTATTATCATACAAA--A
66 AGAGATTTAAGCATCCCTACCTCTTTAGGTATCAATCCA--GAAAACATATTATCA-A-AAAGGA
* *** *
54607248 AAAGA-TGAACCAAGTTGC
127 TAAGAGT-AGTTAAGTTGG
* * *
54607266 TTAAGTTTCCTATCGAAGTAGGGATTTGTCCACAGAATGTGTTATTGGACAGATCCAATTCACTA
1 TCAAGTTTCCTATGGAAGTAGGGATTTGTCCAGAGAATGTGTTATTGGACAGATCCAATTCACTA
* * * *
54607331 AGAGATTTAAGCATCCCTACCTCTTTAGGTATCAATCCAGAAAACATATTTTGAGAAAGGGTAAG
66 AGAGATTTAAGCATCCCTACCTCTTTAGGTATCAATCCAGAAAACATATTATCAAAAAGGATAAG
*
54607396 AGTAGTTAAGCTGG
131 AGTAGTTAAGTTGG
54607410 TCA
1 TCA
54607413 TGCTCCCTAT
Statistics
Matches: 239, Mismatches: 42, Indels: 20
0.79 0.14 0.07
Matches are distributed among these distances:
142 4 0.02
143 3 0.01
144 225 0.94
145 4 0.02
146 3 0.01
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (144 bp):
TCAAGTTTCCTATGGAAGTAGGGATTTGTCCAGAGAATGTGTTATTGGACAGATCCAATTCACTA
AGAGATTTAAGCATCCCTACCTCTTTAGGTATCAATCCAGAAAACATATTATCAAAAAGGATAAG
AGTAGTTAAGTTGG
Found at i:54610398 original size:21 final size:21
Alignment explanation
Indices: 54610372--54610412 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
54610362 ATCTGCTCAA
* *
54610372 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
54610393 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
54610413 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:54613863 original size:111 final size:111
Alignment explanation
Indices: 54613669--54613891 Score: 392
Period size: 111 Copynumber: 2.0 Consensus size: 111
54613659 AATTCTAAGA
*
54613669 TCATTTGAATTTATCATTGTGAGCAAAGCTTTGATCTTTTAGTTTATTTATTTGTCATCCTACCA
1 TCATTTGAATTTATAATTGTGAGCAAAGCTTTGATCTTTTAGTTTATTTATTTGTCATCCTACCA
* *
54613734 TCATCAAATCTTGATTGTAGCTAAAATGTCACTATATTTAGTAAAT
66 TCATCAAATATTGATTGTAGCTAAAATGTCACTATATTCAGTAAAT
*
54613780 TCATTTGAATTTATAATTGTGAGCAAAGCTTTGATCTTTTAGTTTATTTATTTGTCATCCTATCA
1 TCATTTGAATTTATAATTGTGAGCAAAGCTTTGATCTTTTAGTTTATTTATTTGTCATCCTACCA
* *
54613845 TCATTAAATATTGATTGTAGTTAAAATGTCACTATATTCAGTAAAT
66 TCATCAAATATTGATTGTAGCTAAAATGTCACTATATTCAGTAAAT
54613891 T
1 T
54613892 TAATTTTTTT
Statistics
Matches: 106, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
111 106 1.00
ACGTcount: A:0.30, C:0.13, G:0.12, T:0.45
Consensus pattern (111 bp):
TCATTTGAATTTATAATTGTGAGCAAAGCTTTGATCTTTTAGTTTATTTATTTGTCATCCTACCA
TCATCAAATATTGATTGTAGCTAAAATGTCACTATATTCAGTAAAT
Found at i:54617386 original size:21 final size:21
Alignment explanation
Indices: 54617357--54617397 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
54617347 AATATTTAAA
*
54617357 TTCAAAAAATTATTAAAAAAG
1 TTCAAAAAAGTATTAAAAAAG
* *
54617378 TTCATAAAAGTCTTAAAAAA
1 TTCAAAAAAGTATTAAAAAA
54617398 TTAGCATGAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.59, C:0.07, G:0.05, T:0.29
Consensus pattern (21 bp):
TTCAAAAAAGTATTAAAAAAG
Found at i:54622729 original size:37 final size:37
Alignment explanation
Indices: 54622688--54622762 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
54622678 TGAGAAAAAA
54622688 GTTAGAAAAATTCAAACTGTAGGAGTCACATGGCTGG
1 GTTAGAAAAATTCAAACTGTAGGAGTCACATGGCTGG
54622725 GTTAGAAAAATTCAAACTGTAGGAGTCACATGGCTGG
1 GTTAGAAAAATTCAAACTGTAGGAGTCACATGGCTGG
54622762 G
1 G
54622763 ACACACGCCC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.35, C:0.13, G:0.28, T:0.24
Consensus pattern (37 bp):
GTTAGAAAAATTCAAACTGTAGGAGTCACATGGCTGG
Found at i:54633772 original size:14 final size:14
Alignment explanation
Indices: 54633727--54633775 Score: 53
Period size: 14 Copynumber: 3.3 Consensus size: 14
54633717 ACACGACAAC
54633727 ATTAAATATTAAAA
1 ATTAAATATTAAAA
*
54633741 ATCATAAAATATAAAAA
1 AT--T-AAATATTAAAA
*
54633758 ATTAAATATTTAAA
1 ATTAAATATTAAAA
54633772 ATTA
1 ATTA
54633776 TTAAAATGGA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
14 15 0.52
15 1 0.03
16 1 0.03
17 12 0.41
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (14 bp):
ATTAAATATTAAAA
Found at i:54633778 original size:17 final size:17
Alignment explanation
Indices: 54633727--54633780 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 17
54633717 ACACGACAAC
* *
54633727 ATTAAATATTAAAAATC
1 ATTAAATATTTAAAATA
*
54633744 A-TAAA-ATATAAAA-A
1 ATTAAATATTTAAAATA
*
54633758 ATTAAATATTTAAAATT
1 ATTAAATATTTAAAATA
54633775 ATTAAA
1 ATTAAA
54633781 ATGGACACAA
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
14 1 0.03
15 10 0.34
16 11 0.38
17 7 0.24
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (17 bp):
ATTAAATATTTAAAATA
Found at i:54633850 original size:26 final size:28
Alignment explanation
Indices: 54633794--54633852 Score: 77
Period size: 26 Copynumber: 2.2 Consensus size: 28
54633784 GACACAAATT
* * *
54633794 TAAAAATTATAAAAACTTATACATATTA
1 TAAAAATTATAAAAACCTATACAAATCA
54633822 TAAAAA-TATAAAAACCTA-ACAAATCA
1 TAAAAATTATAAAAACCTATACAAATCA
54633848 TAAAA
1 TAAAA
54633853 GTTTTATAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 11 0.39
27 11 0.39
28 6 0.21
ACGTcount: A:0.63, C:0.10, G:0.00, T:0.27
Consensus pattern (28 bp):
TAAAAATTATAAAAACCTATACAAATCA
Found at i:54633920 original size:17 final size:17
Alignment explanation
Indices: 54633891--54634021 Score: 63
Period size: 19 Copynumber: 7.3 Consensus size: 17
54633881 CAATTTTATG
54633891 AAAATCATA-AAATATTA
1 AAAAT-ATATAAATATTA
*
54633908 AAAATATATAAATTAGTA
1 AAAATATATAAA-TATTA
*
54633926 AAAA-ATATAAAAACTTA
1 AAAATATATAAATA-TTA
* *
54633943 TAAATATTATAAAAATATA
1 AAAATA-TATAAATAT-TA
*
54633962 AAAAT-TA-AAATTTTATA
1 AAAATATATAAA-TAT-TA
* *
54633979 AAAACATATAAAAATTCA
1 AAAATATATAAATATT-A
*
54633997 TAAAAAATATAAATAATATA
1 -AAAATATATAAAT-AT-TA
54634017 AAAAT
1 AAAAT
54634022 TCTAATAAAT
Statistics
Matches: 88, Mismatches: 13, Indels: 24
0.70 0.10 0.19
Matches are distributed among these distances:
16 7 0.08
17 31 0.35
18 14 0.16
19 32 0.36
20 3 0.03
21 1 0.01
ACGTcount: A:0.66, C:0.03, G:0.01, T:0.31
Consensus pattern (17 bp):
AAAATATATAAATATTA
Found at i:54633944 original size:10 final size:9
Alignment explanation
Indices: 54633789--54634055 Score: 142
Period size: 9 Copynumber: 29.3 Consensus size: 9
54633779 AAATGGACAC
54633789 AAATT-TAA
1 AAATTATAA
54633797 AAATTATAA
1 AAATTATAA
*
54633806 AAACTTATAC
1 AAA-TTATAA
*
54633816 ATATTATAA
1 AAATTATAA
54633825 AAA-TATAA
1 AAATTATAA
* *
54633833 AAACCTA-AC
1 AAA-TTATAA
*
54633842 AAATCATAA
1 AAATTATAA
* *
54633851 AAGTTTTATA
1 AAATTATA-A
54633861 AAATTAATAAA
1 AAATT-AT-AA
*
54633872 AAATATTTACA
1 AAAT-TATA-A
** *
54633883 ATTTTATGA
1 AAATTATAA
*
54633892 AAATCAT-A
1 AAATTATAA
54633900 AAA-TATTAA
1 AAATTA-TAA
*
54633909 AAA-TATAT
1 AAATTATAA
54633917 AAATTAGTAA
1 AAATTA-TAA
*
54633927 AAAATATAA
1 AAATTATAA
54633936 AAACTTATAA
1 AAA-TTATAA
*
54633946 ATATTATAA
1 AAATTATAA
54633955 AAA-TATAA
1 AAATTATAA
54633963 AAATTA-AA
1 AAATTATAA
**
54633971 ATTTTATAA
1 AAATTATAA
*
54633980 AAACATATAA
1 AAA-TTATAA
54633990 AAATTCATAA
1 AAATT-ATAA
*
54634000 AAAATATAA
1 AAATTATAA
54634009 ATAA-TATAA
1 A-AATTATAA
*
54634018 AAATTCTAA
1 AAATTATAA
*
54634027 TAAATTGTAA
1 -AAATTATAA
54634037 AAA--ATAA
1 AAATTATAA
54634044 AAATTATAA
1 AAATTATAA
54634053 AAA
1 AAA
54634056 CTTGTCGAAA
Statistics
Matches: 197, Mismatches: 38, Indels: 47
0.70 0.13 0.17
Matches are distributed among these distances:
7 7 0.04
8 40 0.20
9 81 0.41
10 57 0.29
11 10 0.05
12 2 0.01
ACGTcount: A:0.62, C:0.04, G:0.01, T:0.32
Consensus pattern (9 bp):
AAATTATAA
Found at i:54633961 original size:44 final size:45
Alignment explanation
Indices: 54633891--54634012 Score: 126
Period size: 44 Copynumber: 2.7 Consensus size: 45
54633881 CAATTTTATG
* *
54633891 AAAATCATA-AAATATTA-AAAATATATAAATTAGTAAAA-AATAT
1 AAAAACATATAAATATTATAAAA-ATATAAATAAGTAAAATAATAT
* * **
54633934 AAAAACTTATAAATATTATAAAAATATAAA-AATTAAAATTTTAT
1 AAAAACATATAAATATTATAAAAATATAAATAAGTAAAATAATAT
*
54633978 AAAAACATATAAAAATTCATAAAAAATATAAATAA
1 AAAAACATATAAATATT-AT-AAAAATATAAATAA
54634013 TATAAAAATT
Statistics
Matches: 65, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
43 13 0.20
44 33 0.51
45 6 0.09
46 11 0.17
47 2 0.03
ACGTcount: A:0.66, C:0.03, G:0.01, T:0.30
Consensus pattern (45 bp):
AAAAACATATAAATATTATAAAAATATAAATAAGTAAAATAATAT
Found at i:54633994 original size:21 final size:19
Alignment explanation
Indices: 54633907--54634055 Score: 97
Period size: 19 Copynumber: 8.2 Consensus size: 19
54633897 ATAAAATATT
*
54633907 AAAAATATATAAATT-AGTA
1 AAAAATATAAAAATTCA-TA
54633926 AAAAATATAAAAACTT-ATA
1 AAAAATATAAAAA-TTCATA
* *
54633945 AATATTATAAAAA-T-AT-
1 AAAAATATAAAAATTCATA
* *
54633961 AAAAAT-TAAAATTTTATA
1 AAAAATATAAAAATTCATA
54633979 AAAACATATAAAAATTCATA
1 AAAA-ATATAAAAATTCATA
54633999 AAAAATATAAATAA-T-ATA
1 AAAAATATAAA-AATTCATA
* * *
54634017 AAAATTCTAATAAATT-GT-
1 AAAAATATAA-AAATTCATA
54634035 AAAAA-ATAAAAATT-ATA
1 AAAAATATAAAAATTCATA
54634052 AAAA
1 AAAA
54634056 CTTGTCGAAA
Statistics
Matches: 106, Mismatches: 14, Indels: 22
0.75 0.10 0.15
Matches are distributed among these distances:
15 5 0.05
16 11 0.10
17 12 0.11
18 21 0.20
19 38 0.36
20 19 0.18
ACGTcount: A:0.66, C:0.03, G:0.01, T:0.30
Consensus pattern (19 bp):
AAAAATATAAAAATTCATA
Found at i:54634004 original size:73 final size:73
Alignment explanation
Indices: 54633899--54634056 Score: 175
Period size: 73 Copynumber: 2.2 Consensus size: 73
54633889 TGAAAATCAT
* * *
54633899 AAAA-TATTAAAA-ATATATAAATTAGTAAAAAATATAAA-AACTTATAAATATTATAA-AAA-T
1 AAAATTATAAAAACATATAAAAATTAGTAAAAAATATAAATAA--TATAAAAATTATAATAAATT
*
54633959 ATAAAAATTA
64 ATAAAAAATA
* *
54633969 AAATTTTATAAAAACATATAAAAATTCA-TAAAAAATATAAATAATATAAAAATTCTAATAAATT
1 AAA-ATTATAAAAACATATAAAAATT-AGTAAAAAATATAAATAATATAAAAATTATAATAAATT
*
54634033 GTAAAAAATA
64 ATAAAAAATA
54634043 AAAATTATAAAAAC
1 AAAATTATAAAAAC
54634057 TTGTCGAAAT
Statistics
Matches: 73, Mismatches: 8, Indels: 11
0.79 0.09 0.12
Matches are distributed among these distances:
70 3 0.04
72 19 0.26
73 36 0.49
74 15 0.21
ACGTcount: A:0.65, C:0.03, G:0.01, T:0.30
Consensus pattern (73 bp):
AAAATTATAAAAACATATAAAAATTAGTAAAAAATATAAATAATATAAAAATTATAATAAATTAT
AAAAAATA
Found at i:54635348 original size:20 final size:22
Alignment explanation
Indices: 54635320--54635366 Score: 62
Period size: 20 Copynumber: 2.2 Consensus size: 22
54635310 TTTTAAGTTA
*
54635320 AAAATTAAAAGAAT-AA-AAAT
1 AAAACTAAAAGAATAAATAAAT
*
54635340 AAAACTAAATGAATAAATAAAT
1 AAAACTAAAAGAATAAATAAAT
54635362 AAAAC
1 AAAAC
54635367 AAACACCCAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 12 0.52
21 2 0.09
22 9 0.39
ACGTcount: A:0.72, C:0.04, G:0.04, T:0.19
Consensus pattern (22 bp):
AAAACTAAAAGAATAAATAAAT
Found at i:54636209 original size:85 final size:85
Alignment explanation
Indices: 54636097--54636395 Score: 287
Period size: 85 Copynumber: 3.5 Consensus size: 85
54636087 GACGAGATTG
* ** * *
54636097 GTGGTTTTAGTCTGCTCCACTGTAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTACTGCA
1 GTGGTTTTAATCCACTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTACTGTA
54636162 ACTTCAGAGAGATAAGATCT
66 ACTTCAGAGAGATAAGATCT
** * * * * * * * * *
54636182 GTGGTTTTAATCCGTTCCATTGCAACTTCAGGGAGATAGGATTGGTTTCTTCAATCTGCTCCATT
1 GTGGTTTTAATCCACTCCACTGCAACTTCAGGGAGATAAGACTAG---ATGCGATCTGCTCTACT
*
54636247 GTAACTTCAGGGAGATAAGAT-T
63 GTAACTTCAGAGAGATAAGATCT
* ** * * *
54636269 G-GTTTCTTCTGTCTACTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATATGCTTTACTG
1 GTGGTT-TT-AATCCACTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTACTG
* *
54636333 TAGCTTCAGAGGGATAAGATCT
64 TAACTTCAGAGAGATAAGATCT
* * *
54636355 GTGGTTTTAATCCACTCTACTACAACTTCAGAGAGATAAGA
1 GTGGTTTTAATCCACTCCACTGCAACTTCAGGGAGATAAGA
54636396 TTGGTTTCTT
Statistics
Matches: 165, Mismatches: 42, Indels: 14
0.75 0.19 0.06
Matches are distributed among these distances:
85 92 0.56
86 7 0.04
87 7 0.04
88 59 0.36
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.32
Consensus pattern (85 bp):
GTGGTTTTAATCCACTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTACTGTA
ACTTCAGAGAGATAAGATCT
Found at i:54636210 original size:44 final size:44
Alignment explanation
Indices: 54636158--54636743 Score: 220
Period size: 44 Copynumber: 13.5 Consensus size: 44
54636148 TCTGCTCTAC
* *
54636158 TGCAACTTCAGAGAGATAAGATCTGTGGTT-TT-AATCCGTTCCAT
1 TGCAACTTCAGGGAGATAAGAT-TG-GGTTCTTCAATCCGCTCCAT
* * *
54636202 TGCAACTTCAGGGAGATAGGATTGGTTTCTTCAATCTGCTCCAT
1 TGCAACTTCAGGGAGATAAGATTGGGTTCTTCAATCCGCTCCAT
* * ** ** *
54636246 TGTAACTTCAGGGAGATAAGATTGGTTTCTTCTGTCTACTCCAC
1 TGCAACTTCAGGGAGATAAGATTGGGTTCTTCAATCCGCTCCAT
* * * * * ** *
54636290 TGCAACTTCAGGGAGATAAGACTAGATGC--GATAT--GCTTTAC
1 TGCAACTTCAGGGAGATAAGATTGGGTTCTTCA-ATCCGCTCCAT
* * * * *
54636331 TGTAGCTTCAGAGG-GATAAGATCTGTGGTT-TT-AATCCACTCTAC
1 TGCAACTTCAG-GGAGATAAGAT-TG-GGTTCTTCAATCCGCTCCAT
* * * ** ** *
54636375 TACAACTTCAGAGAGATAAGATTGGTTTCTTCTGTCTACTCCAC
1 TGCAACTTCAGGGAGATAAGATTGGGTTCTTCAATCCGCTCCAT
** * * * * * * * *
54636419 TATAACTTTAGGGAGATAAGACT-GGAT-GT-GATCTGCTCTAC
1 TGCAACTTCAGGGAGATAAGATTGGGTTCTTCAATCCGCTCCAT
* * * * *
54636460 TCCAACTTTAGAGAGATAAGATCTTGTGGTT-TT-AATCAGCTCCAC
1 TGCAACTTCAGGGAGATAAGA--TTG-GGTTCTTCAATCCGCTCCAT
* * * * ** *
54636505 TGCAACTTCAGTGAGATATGATTTGTTTCTTCAATATGCTCCAC
1 TGCAACTTCAGGGAGATAAGATTGGGTTCTTCAATCCGCTCCAT
* * * * ** ** *
54636549 TGTAACTTTAGGGAGATAAGGTTGGTTTCTTCTGTCTACTCCAC
1 TGCAACTTCAGGGAGATAAGATTGGGTTCTTCAATCCGCTCCAT
* * * * * * *
54636593 TGCAACTTCAGGGAGATAAGACT-GG--ATGCGATCTGCTCTAC
1 TGCAACTTCAGGGAGATAAGATTGGGTTCTTCAATCCGCTCCAT
* *
54636634 TGCAACTTCAGAGAGATAAGATCTTGTGGTT-TT-AATCCGCTCCAC
1 TGCAACTTCAGGGAGATAAGA--TTG-GGTTCTTCAATCCGCTCCAT
* * * * * *
54636679 TGTAACTTTAGGGAGATAGGATTGGTTTCTTCAATCTGCTCCAC
1 TGCAACTTCAGGGAGATAAGATTGGGTTCTTCAATCCGCTCCAT
54636723 TGCAACTTCAGGGAGATAAGA
1 TGCAACTTCAGGGAGATAAGA
54636744 CTTTATGATT
Statistics
Matches: 412, Mismatches: 103, Indels: 54
0.72 0.18 0.09
Matches are distributed among these distances:
41 76 0.18
42 18 0.04
43 27 0.07
44 232 0.56
45 58 0.14
46 1 0.00
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.33
Consensus pattern (44 bp):
TGCAACTTCAGGGAGATAAGATTGGGTTCTTCAATCCGCTCCAT
Found at i:54636340 original size:129 final size:128
Alignment explanation
Indices: 54636204--54636568 Score: 403
Period size: 129 Copynumber: 2.8 Consensus size: 128
54636194 CGTTCCATTG
* * * * * *
54636204 CAACTTCAGGGAGATAGGATTG-GTTTCTTCAATCTGCTCCATTGTAACTTCAGGGAGATAAGAT
1 CAACTTCAGGGAGATAAGATTGTGGTT-TT-AATCAGCTCCACTGCAACTTCAGAGAGATAAGAT
* * * *
54636268 TGGTTTCTTCTGTCTACTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATATGCTTTACTG
64 TGGTTTCTTCTGTCTACTCCACTGTAACTTTAGGGAGATAAGACTAGATGCGATATGCTCTACTC
* * * *
54636333 TAGCTTCAGAGG-GATAAGATCTGTGGTTTTAATCCA-CTCTACTACAACTTCAGAGAGATAAGA
1 CAACTTCAG-GGAGATAAGAT-TGTGGTTTTAAT-CAGCTCCACTGCAACTTCAGAGAGATAAGA
* * * *
54636396 TTGGTTTCTTCTGTCTACTCCACTATAACTTTAGGGAGATAAGACTGGATGTGATCTGCTCTACT
63 TTGGTTTCTTCTGTCTACTCCACTGTAACTTTAGGGAGATAAGACTAGATGCGATATGCTCTACT
54636461 C
128 C
* * * *
54636462 CAACTTTAGAGAGATAAGATCTTGTGGTTTTAATCAGCTCCACTGCAACTTCAGTGAGATATGAT
1 CAACTTCAGGGAGATAAGA--TTGTGGTTTTAATCAGCTCCACTGCAACTTCAGAGAGATAAGAT
* ** * *
54636527 TTGTTTCTTCAATATGCTCCACTGTAACTTTAGGGAGATAAG
64 TGGTTTCTTCTGTCTACTCCACTGTAACTTTAGGGAGATAAG
54636569 GTTGGTTTCT
Statistics
Matches: 196, Mismatches: 32, Indels: 15
0.81 0.13 0.06
Matches are distributed among these distances:
128 1 0.01
129 112 0.57
130 79 0.40
131 4 0.02
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (128 bp):
CAACTTCAGGGAGATAAGATTGTGGTTTTAATCAGCTCCACTGCAACTTCAGAGAGATAAGATTG
GTTTCTTCTGTCTACTCCACTGTAACTTTAGGGAGATAAGACTAGATGCGATATGCTCTACTC
Found at i:54636342 original size:173 final size:173
Alignment explanation
Indices: 54636106--54636439 Score: 488
Period size: 173 Copynumber: 1.9 Consensus size: 173
54636096 GGTGGTTTTA
* * *
54636106 GTCTGCTCCACTGTAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTACTGCAACTTCAGAG
1 GTCTACTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATATGCTCTACTGCAACTTCAGAG
** * * * *
54636171 AGATAAGATCTGTGGTTTTAATCCGTTCCATTGCAACTTCAGGGAGATAGGATTGGTTTCTTCAA
66 AGATAAGATCTGTGGTTTTAATCCACTCCACTACAACTTCAGAGAGATAAGATTGGTTTCTTCAA
* * *
54636236 TCTGCTCCATTGTAACTTCAGGGAGATAAGATTGGTTTCTTCT
131 TCTACTCCACTATAACTTCAGGGAGATAAGATTGGTTTCTTCT
* * *
54636279 GTCTACTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATATGCTTTACTGTAGCTTCAGAG
1 GTCTACTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATATGCTCTACTGCAACTTCAGAG
* * **
54636344 GGATAAGATCTGTGGTTTTAATCCACTCTACTACAACTTCAGAGAGATAAGATTGGTTTCTTCTG
66 AGATAAGATCTGTGGTTTTAATCCACTCCACTACAACTTCAGAGAGATAAGATTGGTTTCTTCAA
*
54636409 TCTACTCCACTATAACTTTAGGGAGATAAGA
131 TCTACTCCACTATAACTTCAGGGAGATAAGA
54636440 CTGGATGTGA
Statistics
Matches: 141, Mismatches: 20, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
173 141 1.00
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.32
Consensus pattern (173 bp):
GTCTACTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATATGCTCTACTGCAACTTCAGAG
AGATAAGATCTGTGGTTTTAATCCACTCCACTACAACTTCAGAGAGATAAGATTGGTTTCTTCAA
TCTACTCCACTATAACTTCAGGGAGATAAGATTGGTTTCTTCT
Found at i:54636579 original size:174 final size:174
Alignment explanation
Indices: 54636377--54636743 Score: 581
Period size: 174 Copynumber: 2.1 Consensus size: 174
54636367 CACTCTACTA
* * *
54636377 CAACTTCAGAGAGATAAGATTGGTTTCTTCTGTCTACTCCACTATAACTTTAGGGAGATAAGACT
1 CAACTTCAGGGAGATAAGATTGGTTTCTTCTGTCTACTCCACTACAACTTCAGGGAGATAAGACT
* *
54636442 GGATGTGATCTGCTCTACTCCAACTTTAGAGAGATAAGATCTTGTGGTTTTAATCAGCTCCACTG
66 GGATGCGATCTGCTCTACTCCAACTTCAGAGAGATAAGATCTTGTGGTTTTAATCAGCTCCACTG
* * *
54636507 CAACTTCAGTGAGATATGATTTGTTTCTTCAATATGCTCCACTG
131 CAACTTCAGGGAGATAGGATTGGTTTCTTCAATATGCTCCACTG
* * * *
54636551 TAACTTTAGGGAGATAAGGTTGGTTTCTTCTGTCTACTCCACTGCAACTTCAGGGAGATAAGACT
1 CAACTTCAGGGAGATAAGATTGGTTTCTTCTGTCTACTCCACTACAACTTCAGGGAGATAAGACT
* *
54636616 GGATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTTGTGGTTTTAATCCGCTCCACTG
66 GGATGCGATCTGCTCTACTCCAACTTCAGAGAGATAAGATCTTGTGGTTTTAATCAGCTCCACTG
* * *
54636681 TAACTTTAGGGAGATAGGATTGGTTTCTTCAATCTGCTCCACTG
131 CAACTTCAGGGAGATAGGATTGGTTTCTTCAATATGCTCCACTG
54636725 CAACTTCAGGGAGATAAGA
1 CAACTTCAGGGAGATAAGA
54636744 CTTTATGATT
Statistics
Matches: 173, Mismatches: 20, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
174 173 1.00
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.33
Consensus pattern (174 bp):
CAACTTCAGGGAGATAAGATTGGTTTCTTCTGTCTACTCCACTACAACTTCAGGGAGATAAGACT
GGATGCGATCTGCTCTACTCCAACTTCAGAGAGATAAGATCTTGTGGTTTTAATCAGCTCCACTG
CAACTTCAGGGAGATAGGATTGGTTTCTTCAATATGCTCCACTG
Found at i:54636676 original size:130 final size:129
Alignment explanation
Indices: 54636498--54636745 Score: 367
Period size: 130 Copynumber: 1.9 Consensus size: 129
54636488 GTTTTAATCA
* * *
54636498 GCTCCACTGCAACTTCAGTGAGATATGATTTGTTTCTTCAATATGCTCCACTGTAACTTTAGGGA
1 GCTCCACTGCAACTTCAGAGAGATAAGATTTGTTTCTTCAATACGCTCCACTGTAACTTTAGGGA
**
54636563 GATAAGG-TTGGTTTCTTCTGTCTACTCCACTGCAACTTCAGGGAGATAAGACTGGATGCGATCT
66 GAT-AGGATTGGTTTCTTCAATCTACTCCACTGCAACTTCAGGGAGATAAGACTGGATGCGATCT
* *
54636627 GCTCTACTGCAACTTCAGAGAGATAAGATCTTGTGGTT-TT-AATCCGCTCCACTGTAACTTTAG
1 GCTCCACTGCAACTTCAGAGAGATAAGAT-TTGT--TTCTTCAATACGCTCCACTGTAACTTTAG
*
54636690 GGAGATAGGATTGGTTTCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACT
63 GGAGATAGGATTGGTTTCTTCAATCTACTCCACTGCAACTTCAGGGAGATAAGACT
54636746 TTATGATTTC
Statistics
Matches: 107, Mismatches: 8, Indels: 7
0.88 0.07 0.06
Matches are distributed among these distances:
129 29 0.27
130 74 0.69
131 2 0.02
132 2 0.02
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.32
Consensus pattern (129 bp):
GCTCCACTGCAACTTCAGAGAGATAAGATTTGTTTCTTCAATACGCTCCACTGTAACTTTAGGGA
GATAGGATTGGTTTCTTCAATCTACTCCACTGCAACTTCAGGGAGATAAGACTGGATGCGATCT
Found at i:54647598 original size:31 final size:31
Alignment explanation
Indices: 54647561--54647623 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
54647551 AAGTTTTTGA
54647561 CCAAAAGACAAAAATTAATCAATTTACGGCT
1 CCAAAAGACAAAAATTAATCAATTTACGGCT
*
54647592 CCAAAAGACAAAAATTAATCAATTTATGGCT
1 CCAAAAGACAAAAATTAATCAATTTACGGCT
54647623 C
1 C
54647624 GGCTCTCTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.48, C:0.19, G:0.10, T:0.24
Consensus pattern (31 bp):
CCAAAAGACAAAAATTAATCAATTTACGGCT
Found at i:54648851 original size:17 final size:17
Alignment explanation
Indices: 54648817--54648864 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 17
54648807 AAGATATGGG
*
54648817 AAATAAATATGT-TACA
1 AAATATATATGTATACA
*
54648833 AAATGTATATGTATACA
1 AAATATATATGTATACA
*
54648850 AAATATAAATGTATA
1 AAATATATATGTATA
54648865 TGCATATACA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
16 10 0.37
17 17 0.63
ACGTcount: A:0.54, C:0.04, G:0.08, T:0.33
Consensus pattern (17 bp):
AAATATATATGTATACA
Found at i:54649011 original size:3 final size:3
Alignment explanation
Indices: 54649003--54649053 Score: 66
Period size: 3 Copynumber: 16.7 Consensus size: 3
54648993 CGTACGTGGA
* * *
54649003 AAT AAT AAT TAT AAT ACT AAT AAT AAT AGT AAAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT
54649049 AAT AA
1 AAT AA
54649054 ATTTTCTTTA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
3 39 0.95
4 2 0.05
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:54649701 original size:20 final size:22
Alignment explanation
Indices: 54649673--54649719 Score: 62
Period size: 20 Copynumber: 2.2 Consensus size: 22
54649663 TTTTAAGTTA
*
54649673 AAAATTAAAAGAAT-AA-AAAT
1 AAAACTAAAAGAATAAATAAAT
*
54649693 AAAACTAAATGAATAAATAAAT
1 AAAACTAAAAGAATAAATAAAT
54649715 AAAAC
1 AAAAC
54649720 AAACACCCAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 12 0.52
21 2 0.09
22 9 0.39
ACGTcount: A:0.72, C:0.04, G:0.04, T:0.19
Consensus pattern (22 bp):
AAAACTAAAAGAATAAATAAAT
Found at i:54650292 original size:9 final size:9
Alignment explanation
Indices: 54650253--54650542 Score: 125
Period size: 9 Copynumber: 31.4 Consensus size: 9
54650243 AACCATAATT
*
54650253 AAAATTATT
1 AAAATTATA
*
54650262 AAAATGGATA
1 AAAAT-TATA
*
54650272 CAAATT-TA
1 AAAATTATA
54650280 AAAATTATA
1 AAAATTATA
54650289 AAAACTTATA
1 AAAA-TTATA
* *
54650299 AATATTACA
1 AAAATTATA
54650308 AAAA-TATAA
1 AAAATTAT-A
*
54650317 AAAATCAT-
1 AAAATTATA
*
54650325 AAAATCATA
1 AAAATTATA
* *
54650334 AAATTTTTA
1 AAAATTATA
54650343 TAAAATTAATAA
1 -AAAATT-AT-A
*
54650355 AAAATATTTA
1 AAAAT-TATA
** *
54650365 CAATTTTATG
1 -AAAATTATA
*
54650375 AAAATCAT-
1 AAAATTATA
54650383 AAAA-TATTA
1 AAAATTA-TA
54650392 AAAA-TAT-
1 AAAATTATA
54650399 -AAATTAGTA
1 AAAATTA-TA
*
54650408 AAAAATATA
1 AAAATTATA
54650417 AAAACTTATA
1 AAAA-TTATA
*
54650427 AATATTATA
1 AAAATTATA
54650436 AAAA-TATA
1 AAAATTATA
*
54650444 ATAATTA-A
1 AAAATTATA
**
54650452 AATTTTATA
1 AAAATTATA
*
54650461 AAAACATATA
1 AAAA-TTATA
54650471 AAAATTCATAAAA
1 AAAATT-AT---A
54650484 AAAATTATA
1 AAAATTATA
54650493 AATAA-TATA
1 AA-AATTATA
* *
54650502 AAATTTCTA
1 AAAATTATA
54650511 ATAAATTATA
1 A-AAATTATA
**
54650521 AAAAAAATA
1 AAAATTATA
54650530 AAAATTATA
1 AAAATTATA
54650539 AAAA
1 AAAA
54650543 CTCATTTAAA
Statistics
Matches: 209, Mismatches: 44, Indels: 56
0.68 0.14 0.18
Matches are distributed among these distances:
6 3 0.01
7 3 0.01
8 37 0.18
9 90 0.43
10 55 0.26
11 10 0.05
12 4 0.02
13 7 0.03
ACGTcount: A:0.62, C:0.04, G:0.01, T:0.32
Consensus pattern (9 bp):
AAAATTATA
Found at i:54650292 original size:10 final size:10
Alignment explanation
Indices: 54650279--54650542 Score: 72
Period size: 10 Copynumber: 26.4 Consensus size: 10
54650269 ATACAAATTT
54650279 AAAAATTATA
1 AAAAATTATA
*
54650289 AAAACTTAT-
1 AAAAATTATA
* *
54650298 AAATATTA-C
1 AAAAATTATA
54650307 AAAAA-TATA
1 AAAAATTATA
*
54650316 AAAAATCAT-
1 AAAAATTATA
*
54650325 -AAAATCAT-
1 AAAAATTATA
* *
54650333 AAAATTTTTA
1 AAAAATTATA
*
54650343 TAAAATTAATA
1 AAAAATT-ATA
*
54650354 AAAAA-TATT
1 AAAAATTATA
* * *
54650363 TACAATTTTA
1 AAAAATTATA
* *
54650373 TGAAAATCATA
1 -AAAAATTATA
* *
54650384 AAATATTAAAA
1 AAAAATT-ATA
54650395 ATATAAATTAGTA
1 A-A-AAATTA-TA
54650408 AAAAA-TATA
1 AAAAATTATA
*
54650417 AAAACTTAT-
1 AAAAATTATA
*
54650426 AAATATTATA
1 AAAAATTATA
*
54650436 AAAATATAATA
1 AAAA-ATTATA
54650447 ATTAAAATTTTATA
1 A--AAAA--TTATA
54650461 AAAACA-TAT-
1 AAAA-ATTATA
54650470 AAAAATTCATAAA
1 AAAAATT-AT--A
54650483 AAAAATTATA
1 AAAAATTATA
*
54650493 AATAA-TAT-
1 AAAAATTATA
* *
54650501 AAAATTTCTA
1 AAAAATTATA
*
54650511 ATAAATTATA
1 AAAAATTATA
*
54650521 AAAAA-AAT-
1 AAAAATTATA
54650529 AAAAATTATA
1 AAAAATTATA
54650539 AAAA
1 AAAA
54650543 CTCATTTAAA
Statistics
Matches: 181, Mismatches: 44, Indels: 58
0.64 0.16 0.20
Matches are distributed among these distances:
8 19 0.10
9 52 0.29
10 55 0.30
11 24 0.13
12 9 0.05
13 17 0.09
14 5 0.03
ACGTcount: A:0.63, C:0.04, G:0.01, T:0.32
Consensus pattern (10 bp):
AAAAATTATA
Found at i:54650400 original size:16 final size:17
Alignment explanation
Indices: 54650375--54650419 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
54650365 CAATTTTATG
*
54650375 AAAATCATAAAATA-TTA
1 AAAAT-ATAAAATAGTAA
*
54650392 AAAATATAAATTAGTAA
1 AAAATATAAAATAGTAA
54650409 AAAATATAAAA
1 AAAATATAAAA
54650420 ACTTATAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 7 0.29
17 17 0.71
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (17 bp):
AAAATATAAAATAGTAA
Found at i:54650441 original size:44 final size:44
Alignment explanation
Indices: 54650390--54650504 Score: 114
Period size: 44 Copynumber: 2.7 Consensus size: 44
54650380 CATAAAATAT
* *
54650390 TAAAAATATAAATTAGTAAAAAATATAAAAACTTATAAATATT-A
1 TAAAAATATAAATTA-TAAAAAATATAAAAACATATAAAAATTCA
***
54650434 TAAAAATATAATAATTA-AAATTTTATAAAAACATATAAAAATTCA
1 TAAAAATAT-A-AATTATAAAAAATATAAAAACATATAAAAATTCA
*
54650479 T-AAAA-A-AAATTATAAATAATATAAAA
1 TAAAAATATAAATTATAAAAAATATAAAA
54650505 TTTCTAATAA
Statistics
Matches: 60, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
40 5 0.08
41 12 0.20
43 1 0.02
44 34 0.57
45 3 0.05
46 5 0.08
ACGTcount: A:0.65, C:0.03, G:0.01, T:0.31
Consensus pattern (44 bp):
TAAAAATATAAATTATAAAAAATATAAAAACATATAAAAATTCA
Found at i:54650485 original size:21 final size:19
Alignment explanation
Indices: 54650391--54650542 Score: 83
Period size: 19 Copynumber: 8.2 Consensus size: 19
54650381 ATAAAATATT
54650391 AAAAATAT--AAATTAGT-A
1 AAAAATATAAAAATTA-TAA
54650408 AAAAATATAAAAACTTAT-A
1 AAAAATATAAAAA-TTATAA
* *
54650427 AATATTATAAAAA-TAT--
1 AAAAATATAAAAATTATAA
* *
54650443 AATAAT-TAAAATTTTATAA
1 AAAAATATAAAA-ATTATAA
*
54650462 AAACATATAAAAATTCATAAA
1 AAAAATATAAAAATT-AT-AA
54650483 AAAAATTATAAATAA-TAT-A
1 AAAAA-TATAAA-AATTATAA
** *
54650502 AAATTTCTAATAAATTATAA
1 AAAAATATAA-AAATTATAA
54650522 AAAAA-ATAAAAATTATAA
1 AAAAATATAAAAATTATAA
54650540 AAA
1 AAA
54650543 CTCATTTAAA
Statistics
Matches: 106, Mismatches: 14, Indels: 29
0.71 0.09 0.19
Matches are distributed among these distances:
15 5 0.05
16 5 0.05
17 14 0.13
18 18 0.17
19 33 0.31
20 14 0.13
21 8 0.08
22 7 0.07
23 2 0.02
ACGTcount: A:0.66, C:0.03, G:0.01, T:0.31
Consensus pattern (19 bp):
AAAAATATAAAAATTATAA
Found at i:54650525 original size:86 final size:86
Alignment explanation
Indices: 54650353--54650536 Score: 191
Period size: 86 Copynumber: 2.2 Consensus size: 86
54650343 TAAAATTAAT
* * * *
54650353 AAAA-AATATTTACAATTTTATGAAAATCATAAAATATTAAAAATATAAATTAGTAAAAAATATA
1 AAAATAATAATTAAAATTTTATGAAAAACATAAAAAATTAAAAATATAAATTAGTAAAAAATATA
*
54650417 AAAACTTATAAATATTATAAA
66 AAAACTTATAAAAATTATAAA
* *
54650438 AATATAATAATTAAAATTTTAT-AAAAACATATAAAAATTCATAAAA-A-AAATTA-TAAATAAT
1 AAAATAATAATTAAAATTTTATGAAAAACATA-AAAAATT-A-AAAATATAAATTAGTAAAAAAT
* *
54650499 AT-AAAATTTCTAATAAATTATAAAA
63 ATAAAAACTTATAA-AAATTAT-AAA
*
54650524 AAAATAAAAATTA
1 AAAATAATAATTA
54650537 TAAAAACTCA
Statistics
Matches: 82, Mismatches: 11, Indels: 11
0.79 0.11 0.11
Matches are distributed among these distances:
84 9 0.11
85 26 0.32
86 41 0.50
87 2 0.02
88 4 0.05
ACGTcount: A:0.63, C:0.03, G:0.01, T:0.33
Consensus pattern (86 bp):
AAAATAATAATTAAAATTTTATGAAAAACATAAAAAATTAAAAATATAAATTAGTAAAAAATATA
AAAACTTATAAAAATTATAAA
Done.