Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008464.1 Hibiscus syriacus cultivar Beakdansim tig00111277_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 593006
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 4
Found at i:182595 original size:14 final size:14
Alignment explanation
Indices: 182576--182602 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
182566 GTATCAGGTA
182576 TGTATGTATGTATG
1 TGTATGTATGTATG
182590 TGTATGTATGTAT
1 TGTATGTATGTAT
182603 ATACTTTTCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.00, G:0.26, T:0.52
Consensus pattern (14 bp):
TGTATGTATGTATG
Found at i:190644 original size:3 final size:3
Alignment explanation
Indices: 190636--190699 Score: 71
Period size: 3 Copynumber: 22.0 Consensus size: 3
190626 GCAAAAATTG
* **
190636 TAA TAA TAAA TAA TAA TAA -AA TAA TAA -GA TAA CGA TAA TAA TAA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
190680 TAA TAA TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA
190700 CGGAAAAAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
2 5 0.10
3 43 0.84
4 3 0.06
ACGTcount: A:0.67, C:0.02, G:0.03, T:0.28
Consensus pattern (3 bp):
TAA
Found at i:190691 original size:32 final size:32
Alignment explanation
Indices: 190638--190701 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
190628 AAAAATTGTA
*
190638 ATAATAAATAATAATAAAATAATAAGATAACG
1 ATAATAAATAATAATAAAATAATAAAATAACG
190670 ATAAT-AATAATAATAATAATAATAAAATAACG
1 ATAATAAATAATAATAA-AATAATAAAATAACG
190702 GAAAAAAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 11 0.37
32 19 0.63
ACGTcount: A:0.66, C:0.03, G:0.05, T:0.27
Consensus pattern (32 bp):
ATAATAAATAATAATAAAATAATAAAATAACG
Found at i:195252 original size:15 final size:17
Alignment explanation
Indices: 195232--195263 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
195222 TCCTATGGTA
195232 GAAGAAG-GG-TCAGAT
1 GAAGAAGAGGTTCAGAT
195247 GAAGAAGAGGTTCAGAT
1 GAAGAAGAGGTTCAGAT
195264 CCAAGAACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 2 0.13
17 6 0.40
ACGTcount: A:0.41, C:0.06, G:0.38, T:0.16
Consensus pattern (17 bp):
GAAGAAGAGGTTCAGAT
Found at i:199995 original size:21 final size:21
Alignment explanation
Indices: 199969--200008 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
199959 GACTATAGCA
199969 TTGCGATTTCCCAAATTCGTG
1 TTGCGATTTCCCAAATTCGTG
* *
199990 TTGCGATTTTCCTAATTCG
1 TTGCGATTTCCCAAATTCG
200009 CAATGCGAAT
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:0.17, C:0.23, G:0.17, T:0.42
Consensus pattern (21 bp):
TTGCGATTTCCCAAATTCGTG
Found at i:200027 original size:20 final size:21
Alignment explanation
Indices: 199966--200357 Score: 416
Period size: 20 Copynumber: 19.1 Consensus size: 21
199956 TCTGACTATA
* **
199966 GCATTGCGATTTCCCAAATTC
1 GCATTGCGATTTACGTAATTC
** * *
199987 GTGTTGCGATTTTCCTAATTC
1 GCATTGCGATTTACGTAATTC
* *
200008 GCAATGCGA-ATACGTAATTC
1 GCATTGCGATTTACGTAATTC
200028 GCATTGCGATTTACGTAA-TC
1 GCATTGCGATTTACGTAATTC
* *
200048 GCATTGCGATTTTCCTAATTC
1 GCATTGCGATTTACGTAATTC
200069 GCATTGCGATTTACGTAA-TC
1 GCATTGCGATTTACGTAATTC
* *
200089 GCATTGCGATTTTCCTAATTC
1 GCATTGCGATTTACGTAATTC
200110 GCATTGCGATTTACGTAA-TC
1 GCATTGCGATTTACGTAATTC
* *
200130 GCATTGCGATTTTCCTAATTC
1 GCATTGCGATTTACGTAATTC
* *
200151 GCATTACGATTTTTC-TAATTC
1 GCATTGCGA-TTTACGTAATTC
*
200172 GCATTGCGATTTACGTAA-CC
1 GCATTGCGATTTACGTAATTC
200192 GCATTGCGATTTACGTAA-TC
1 GCATTGCGATTTACGTAATTC
*
200212 GCATTGCGATTTACGCAATT-
1 GCATTGCGATTTACGTAATTC
* *
200232 TCATTACGATTTTAC-TAATTC
1 GCATTGCGA-TTTACGTAATTC
200253 GCATTGCGATTTACGTAATT-
1 GCATTGCGATTTACGTAATTC
200273 GCATTGCGATTTTAC-TAATTC
1 GCATTGCGA-TTTACGTAATTC
* * *
200294 GCATTACGATTTTCCTAATTC
1 GCATTGCGATTTACGTAATTC
*
200315 GTACTT-CGATTTACGTAA-TC
1 GCA-TTGCGATTTACGTAATTC
*
200335 GCATTGCGATTTA-GTAAATC
1 GCATTGCGATTTACGTAATTC
200355 GCA
1 GCA
200358 ACGAGATTCT
Statistics
Matches: 316, Mismatches: 39, Indels: 33
0.81 0.10 0.09
Matches are distributed among these distances:
19 6 0.02
20 161 0.51
21 142 0.45
22 7 0.02
ACGTcount: A:0.24, C:0.21, G:0.16, T:0.39
Consensus pattern (21 bp):
GCATTGCGATTTACGTAATTC
Found at i:200030 original size:82 final size:83
Alignment explanation
Indices: 199966--200357 Score: 480
Period size: 82 Copynumber: 4.8 Consensus size: 83
199956 TCTGACTATA
* * ** * * *
199966 GCATTGCGATTTCCCAAATTCGTGTTGCGATTTTCCTAATTCGCAATGCGA-ATACGTAATTCGC
1 GCATTGCGATTTTCCTAATTCGCATTACGATTTTCCTAATTCGCATTGCGATTTACGTAATTCGC
200030 ATTGCGATTTACGTAATC
66 ATTGCGATTTACGTAATC
* * * * *
200048 GCATTGCGATTTTCCTAATTCGCATTGCGATTTACGTAA-TCGCATTGCGATTTTCCTAATTCGC
1 GCATTGCGATTTTCCTAATTCGCATTACGATTTTCCTAATTCGCATTGCGATTTACGTAATTCGC
200112 ATTGCGATTTACGTAATC
66 ATTGCGATTTACGTAATC
* *
200130 GCATTGCGATTTTCCTAATTCGCATTACGATTTTTCTAATTCGCATTGCGATTTACGTAA-CCGC
1 GCATTGCGATTTTCCTAATTCGCATTACGATTTTCCTAATTCGCATTGCGATTTACGTAATTCGC
200194 ATTGCGATTTACGTAATC
66 ATTGCGATTTACGTAATC
* * *
200212 GCATTGCGATTTACGC-AATT-TCATTACGATTTTACTAATTCGCATTGCGATTTACGTAATT-G
1 GCATTGCGATTTTC-CTAATTCGCATTACGATTTTCCTAATTCGCATTGCGATTTACGTAATTCG
200274 CATTGCGATTTTAC-TAATTC
65 CATTGCGA-TTTACGTAA-TC
* * * * *
200294 GCATTACGATTTTCCTAATTCGTACTT-CGATTTACGTAA-TCGCATTGCGATTTA-GTAAATCG
1 GCATTGCGATTTTCCTAATTCGCA-TTACGATTTTCCTAATTCGCATTGCGATTTACGTAATTCG
200356 CA
65 CA
200358 ACGAGATTCT
Statistics
Matches: 271, Mismatches: 29, Indels: 20
0.85 0.09 0.06
Matches are distributed among these distances:
81 65 0.24
82 175 0.65
83 29 0.11
84 2 0.01
ACGTcount: A:0.24, C:0.21, G:0.16, T:0.39
Consensus pattern (83 bp):
GCATTGCGATTTTCCTAATTCGCATTACGATTTTCCTAATTCGCATTGCGATTTACGTAATTCGC
ATTGCGATTTACGTAATC
Found at i:200067 original size:41 final size:41
Alignment explanation
Indices: 199966--200347 Score: 422
Period size: 41 Copynumber: 9.3 Consensus size: 41
199956 TCTGACTATA
* * ** * *
199966 GCATTGCGATTTCCCAAATTCGTGTTGCGATTTTCCTAATTC
1 GCATTGCGATTTACCTAATTCGCATTGCGATTTACGTAA-TC
* * *
200008 GCAATGCGA-ATACGTAATTCGCATTGCGATTTACGTAATC
1 GCATTGCGATTTACCTAATTCGCATTGCGATTTACGTAATC
*
200048 GCATTGCGATTTTCCTAATTCGCATTGCGATTTACGTAATC
1 GCATTGCGATTTACCTAATTCGCATTGCGATTTACGTAATC
*
200089 GCATTGCGATTTTCCTAATTCGCATTGCGATTTACGTAATC
1 GCATTGCGATTTACCTAATTCGCATTGCGATTTACGTAATC
* * *
200130 GCATTGCGATTTTCCTAATTCGCATTACGATTTTTC-TAATTC
1 GCATTGCGATTTACCTAATTCGCATTGCGA-TTTACGTAA-TC
* *
200172 GCATTGCGATTTACGTAA-CCGCATTGCGATTTACGTAATC
1 GCATTGCGATTTACCTAATTCGCATTGCGATTTACGTAATC
* *
200212 GCATTGCGATTTACGC-AATT-TCATTACGATTTTAC-TAATTC
1 GCATTGCGATTTAC-CTAATTCGCATTGCGA-TTTACGTAA-TC
*
200253 GCATTGCGATTTACGTAATT-GCATTGCGATTTTAC-TAATTC
1 GCATTGCGATTTACCTAATTCGCATTGCGA-TTTACGTAA-TC
* * *
200294 GCATTACGATTTTCCTAATTCGTACTT-CGATTTACGTAATC
1 GCATTGCGATTTACCTAATTCGCA-TTGCGATTTACGTAATC
200335 GCATTGCGATTTA
1 GCATTGCGATTTA
200348 GTAAATCGCA
Statistics
Matches: 295, Mismatches: 33, Indels: 25
0.84 0.09 0.07
Matches are distributed among these distances:
40 42 0.14
41 213 0.72
42 38 0.13
43 2 0.01
ACGTcount: A:0.24, C:0.21, G:0.16, T:0.39
Consensus pattern (41 bp):
GCATTGCGATTTACCTAATTCGCATTGCGATTTACGTAATC
Found at i:200355 original size:143 final size:143
Alignment explanation
Indices: 199990--200357 Score: 526
Period size: 143 Copynumber: 2.6 Consensus size: 143
199980 CAAATTCGTG
* * * * *
199990 TTGCGATTTTCCTAATTCGCAATGCGA-ATACGTAATTCGCATTGCGATTTACGTAATCGCATTG
1 TTGCGATTTTCCTAATTCGCATTACGATTTTCCTAATTCGCATTGCGATTTACGTAATCGCATTG
** * * * *
200054 CGATTTTCCTAATTCGCATTGCGATTTACGTAATCGCATTGCGATTTTCCTAATTCGCATTGCGA
66 CGA-TTTAGTAAATCGCATTGCGATTTACGCAATCGCATTACGATTTTACTAATTCGCATTGCGA
200119 TTTACGTAATCGCA
130 TTTACGTAATCGCA
* *
200133 TTGCGATTTTCCTAATTCGCATTACGATTTTTCTAATTCGCATTGCGATTTACGTAACCGCATTG
1 TTGCGATTTTCCTAATTCGCATTACGATTTTCCTAATTCGCATTGCGATTTACGTAATCGCATTG
**
200198 CGATTTACGT-AATCGCATTGCGATTTACGCAATTTCATTACGATTTTACTAATTCGCATTGCGA
66 CGATTTA-GTAAATCGCATTGCGATTTACGCAATCGCATTACGATTTTACTAATTCGCATTGCGA
*
200262 TTTACGTAATTGCA
130 TTTACGTAATCGCA
* *
200276 TTGCGATTTTACTAATTCGCATTACGATTTTCCTAATTCGTACTT-CGATTTACGTAATCGCATT
1 TTGCGATTTTCCTAATTCGCATTACGATTTTCCTAATTCGCA-TTGCGATTTACGTAATCGCATT
200340 GCGATTTAGTAAATCGCA
65 GCGATTTAGTAAATCGCA
200358 ACGAGATTCT
Statistics
Matches: 201, Mismatches: 20, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
142 2 0.01
143 161 0.80
144 38 0.19
ACGTcount: A:0.24, C:0.21, G:0.16, T:0.39
Consensus pattern (143 bp):
TTGCGATTTTCCTAATTCGCATTACGATTTTCCTAATTCGCATTGCGATTTACGTAATCGCATTG
CGATTTAGTAAATCGCATTGCGATTTACGCAATCGCATTACGATTTTACTAATTCGCATTGCGAT
TTACGTAATCGCA
Found at i:200395 original size:143 final size:142
Alignment explanation
Indices: 199990--200398 Score: 423
Period size: 143 Copynumber: 2.9 Consensus size: 142
199980 CAAATTCGTG
* * * * * * *
199990 TTGCGATTTTCCTAATTCGCAATGCGA-ATACGTAATTCGCATTGCGATTTACGTAATCGCATTG
1 TTGCGATTTTACTAATTCGCATTACGATTTTCCTAATTCGCATTGCGATTTACGTAACCGCATTG
* * ** * * * * * * *
200054 CGATTTTCCTAATTCGCATTGCGATTTACGTAATCGCATTGCGATTTTCCTAATTCGCATTGCGA
66 CGATTTACGTAA-TCGCAACGAGATTTAC-CAATCGCAATACGAATTTACAAATTCGCATTGCGA
200119 TTTACGTAATCGCA
129 TTTACGTAATCGCA
* *
200133 TTGCGATTTTCCTAATTCGCATTACGATTTTTCTAATTCGCATTGCGATTTACGTAACCGCATTG
1 TTGCGATTTTACTAATTCGCATTACGATTTTCCTAATTCGCATTGCGATTTACGTAACCGCATTG
** * ** * * *
200198 CGATTTACGTAATCGCATTGCGATTTACGCAATTTCATTACGATTTTACTAATTCGCATTGCGAT
66 CGATTTACGTAATCGCAACGAGATTTAC-CAATCGCAATACGAATTTACAAATTCGCATTGCGAT
*
200263 TTACGTAATTGCA
130 TTACGTAATCGCA
* *
200276 TTGCGATTTTACTAATTCGCATTACGATTTTCCTAATTCGTACTT-CGATTTACGTAATCGCATT
1 TTGCGATTTTACTAATTCGCATTACGATTTTCCTAATTCGCA-TTGCGATTTACGTAACCGCATT
*
200340 GCGATTTA-GTAAATCGCAACGAGATTCTGA-CTATCGCAATACTGAATTT-CAAATTCGCA
65 GCGATTTACGT-AATCGCAACGAGATT-T-ACCAATCGCAATAC-GAATTTACAAATTCGCA
200399 ACTCGATTTT
Statistics
Matches: 232, Mismatches: 28, Indels: 12
0.85 0.10 0.04
Matches are distributed among these distances:
142 2 0.01
143 179 0.77
144 50 0.22
145 1 0.00
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.38
Consensus pattern (142 bp):
TTGCGATTTTACTAATTCGCATTACGATTTTCCTAATTCGCATTGCGATTTACGTAACCGCATTG
CGATTTACGTAATCGCAACGAGATTTACCAATCGCAATACGAATTTACAAATTCGCATTGCGATT
TACGTAATCGCA
Found at i:201247 original size:24 final size:24
Alignment explanation
Indices: 201220--201273 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
201210 GTATTCGAAA
201220 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
201244 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
201268 TTTGAT
1 TTTGAT
201274 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:203813 original size:20 final size:20
Alignment explanation
Indices: 203788--203837 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
203778 ATCTTAATGT
203788 CTATCGCAACGCGGAAAT-AA
1 CTATCGCAACGC-GAAATGAA
*
203808 CTATCGCAATGCGAAATGAA
1 CTATCGCAACGCGAAATGAA
*
203828 -AATCGCAACG
1 CTATCGCAACG
203838 AGAGAATCGC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
19 13 0.50
20 13 0.50
ACGTcount: A:0.40, C:0.24, G:0.20, T:0.16
Consensus pattern (20 bp):
CTATCGCAACGCGAAATGAA
Found at i:203832 original size:19 final size:18
Alignment explanation
Indices: 203810--203940 Score: 97
Period size: 19 Copynumber: 7.7 Consensus size: 18
203800 GGAAATAACT
203810 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
*
203829 ATCGCAA-CG--A-GAGA
1 ATCGCAAGCGAAATGAAA
203843 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
*
203862 ATCGCAA-CG--A-GAGA
1 ATCGCAAGCGAAATGAAA
203876 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
**
203895 ATCGCAA-C--AA-GGGA
1 ATCGCAAGCGAAATGAAA
203909 ATCGCAAAGCGAAATGAAA
1 ATCGC-AAGCGAAATGAAA
203928 ATCGCAACGCGAA
1 ATCGCAA-GCGAA
203941 TTTAGTTTTG
Statistics
Matches: 88, Mismatches: 8, Indels: 32
0.69 0.06 0.25
Matches are distributed among these distances:
14 27 0.31
15 6 0.07
16 5 0.06
17 5 0.06
18 6 0.07
19 39 0.44
ACGTcount: A:0.46, C:0.19, G:0.24, T:0.11
Consensus pattern (18 bp):
ATCGCAAGCGAAATGAAA
Found at i:203847 original size:14 final size:14
Alignment explanation
Indices: 203828--203882 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
203818 GCGAAATGAA
203828 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
203842 AATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAG
203861 AATCGCAACGAGAG
1 AATCGCAACGAGAG
203875 AATCGCAA
1 AATCGCAA
203883 TGCGAAATGA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.45, C:0.20, G:0.24, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:203852 original size:33 final size:33
Alignment explanation
Indices: 203810--203936 Score: 227
Period size: 33 Copynumber: 3.8 Consensus size: 33
203800 GGAAATAACT
203810 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
203843 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
203876 ATCGCAATGCGAAATGAAAATCGCAACAAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
203909 ATCGCAAAGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
203937 CGAATTTAGT
Statistics
Matches: 90, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 90 1.00
ACGTcount: A:0.46, C:0.19, G:0.24, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:203958 original size:19 final size:19
Alignment explanation
Indices: 203936--203990 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
203926 AAATCGCAAC
203936 GCGAATTTAGTTTTGCGTT
1 GCGAATTTAGTTTTGCGTT
* *
203955 GCGATTTTAGTTTCGCGTT
1 GCGAATTTAGTTTTGCGTT
*
203974 GCG-ATTTTGTTGTTGCG
1 GCGAATTTAGTT-TTGCG
203991 ATTCTCTCGT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
18 6 0.20
19 24 0.80
ACGTcount: A:0.11, C:0.13, G:0.29, T:0.47
Consensus pattern (19 bp):
GCGAATTTAGTTTTGCGTT
Found at i:203990 original size:14 final size:14
Alignment explanation
Indices: 203965--204010 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
203955 GCGATTTTAG
*
203965 TTTCGCGTTGCGAT
1 TTTCTCGTTGCGAT
* *
203979 TTTGTTGTTGCGAT
1 TTTCTCGTTGCGAT
*
203993 TCTCTCGTTGCGAT
1 TTTCTCGTTGCGAT
204007 TTTC
1 TTTC
204011 CTTTCGCATT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.07, C:0.20, G:0.24, T:0.50
Consensus pattern (14 bp):
TTTCTCGTTGCGAT
Found at i:204149 original size:14 final size:14
Alignment explanation
Indices: 204130--204166 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
204120 CATCAATTAA
204130 ACAAATCAACTTTT
1 ACAAATCAACTTTT
**
204144 ACAAATCGTCTTTT
1 ACAAATCAACTTTT
204158 ACAAATCAA
1 ACAAATCAA
204167 TTAAACAATA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.43, C:0.22, G:0.03, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:205601 original size:42 final size:42
Alignment explanation
Indices: 205555--205634 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 42
205545 TGATGACAGT
* * *
205555 GGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
* * *
205597 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGA
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGA
205635 CAGGCGAGTC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 32 1.00
ACGTcount: A:0.23, C:0.17, G:0.39, T:0.21
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
Found at i:206068 original size:19 final size:19
Alignment explanation
Indices: 206028--206135 Score: 91
Period size: 19 Copynumber: 5.8 Consensus size: 19
206018 AATGGAACTT
*
206028 AAAATCGCAACGTGAAAAATG
1 AAAATCGCAACGCG--AAATG
**
206049 ACTATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAATG
206068 AAAATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAATG
* *
206087 AAAATCACAA--CG--A-C
1 AAAATCGCAACGCGAAATG
**
206101 AAAATCGCAACGCGAAACCA
1 AAAATCGCAACGCGAAA-TG
206121 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
206136 TTATAGTTTC
Statistics
Matches: 72, Mismatches: 9, Indels: 13
0.77 0.10 0.14
Matches are distributed among these distances:
14 9 0.12
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 31 0.43
20 15 0.21
21 11 0.15
ACGTcount: A:0.48, C:0.24, G:0.18, T:0.10
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATG
Found at i:206205 original size:20 final size:19
Alignment explanation
Indices: 206160--206217 Score: 89
Period size: 19 Copynumber: 3.0 Consensus size: 19
206150 TGCGATTTTG
206160 TCGTTGCGATTTTCATTTC
1 TCGTTGCGATTTTCATTTC
* *
206179 GCGTTGCAATTTTCATTCTC
1 TCGTTGCGATTTTCATT-TC
206199 TCGTTGCGATTTTCATTTC
1 TCGTTGCGATTTTCATTTC
206218 AACCAAAAGA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 17 0.50
20 17 0.50
ACGTcount: A:0.12, C:0.22, G:0.16, T:0.50
Consensus pattern (19 bp):
TCGTTGCGATTTTCATTTC
Found at i:206416 original size:94 final size:94
Alignment explanation
Indices: 206306--206681 Score: 575
Period size: 94 Copynumber: 4.1 Consensus size: 94
206296 ATGGATTGCA
* *
206306 TTAC-TTCAACCAAAAGACAAAAAAAAGACAAATACTAACTTCAGAGTATTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAAAAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
206370 TTAGCAGAATTGGCAGCAAACGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
* *
206399 TTACTTTCAACCAAAAGACAAAACAAAGACAAATATTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAAAAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
206464 TTAGCAGAATTGGCAGTAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
*
206493 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAAAAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
* * *
206558 TTAGCAGAATTGACAGCAACCAAATAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
* *
206587 TTAC-TTCAACCAAAAGACAAAACAAAATACAAATACTAACTTCACAGTGTT-AATAA-ACA-A-
1 TTACTTTCAACCAAAAGACAAAA-AAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAG
* *
206647 TTTAGCAGTATTGGCAGCAACCGAATAAAT
65 TTTAGCAGAATTGGCAGCAACCGAACAAAT
206677 TTACT
1 TTACT
206682 AAGCAATCTA
Statistics
Matches: 263, Mismatches: 17, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
90 31 0.12
91 1 0.00
92 3 0.01
93 26 0.10
94 202 0.77
ACGTcount: A:0.48, C:0.18, G:0.11, T:0.22
Consensus pattern (94 bp):
TTACTTTCAACCAAAAGACAAAAAAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
TTAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:208390 original size:19 final size:19
Alignment explanation
Indices: 208326--208424 Score: 135
Period size: 19 Copynumber: 5.1 Consensus size: 19
208316 TCTTTTGGTT
* *
208326 GAAATGAAAATCGCAATGA
1 GAAATGAAAATCGCAACGC
208345 GAGAATGAAAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
208365 GGAAATGACTATCGCAACGC
1 -GAAATGAAAATCGCAACGC
208385 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
208404 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
208423 GA
1 GA
208425 TTTTGGTTTC
Statistics
Matches: 71, Mismatches: 7, Indels: 4
0.87 0.09 0.05
Matches are distributed among these distances:
19 39 0.55
20 30 0.42
21 2 0.03
ACGTcount: A:0.45, C:0.18, G:0.23, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:208442 original size:19 final size:19
Alignment explanation
Indices: 208431--208467 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
208421 GCGATTTTGG
208431 TTTCGCGTTGCGATTCTCA
1 TTTCGCGTTGCGATTCTCA
*
208450 TTTTGCGTTGCGATTCTC
1 TTTCGCGTTGCGATTCTC
208468 TCGTTGCGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.08, C:0.24, G:0.22, T:0.46
Consensus pattern (19 bp):
TTTCGCGTTGCGATTCTCA
Found at i:209072 original size:20 final size:20
Alignment explanation
Indices: 209049--209142 Score: 134
Period size: 20 Copynumber: 4.7 Consensus size: 20
209039 CGATAGTCAG
*
209049 ATTCACATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* *
209069 ATTCGCATTGCGATTTTCCT
1 ATTCGCATTGCGATTTACGT
209089 AATTCGCATTGCGATTTACGT
1 -ATTCGCATTGCGATTTACGT
* *
209110 AATCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
209130 ATTCGCATTGCGA
1 ATTCGCATTGCGA
209143 ATTAGGAAAA
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
20 46 0.72
21 18 0.28
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.38
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:209106 original size:41 final size:40
Alignment explanation
Indices: 209049--209142 Score: 134
Period size: 41 Copynumber: 2.3 Consensus size: 40
209039 CGATAGTCAG
* * *
209049 ATTCACATTGCGATTTACGTATTCGCATTGCGATTTTCCT
1 ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACCT
* *
209089 AATTCGCATTGCGATTTACGTAATCGCGTTGCGATTTACGT
1 -ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACCT
209130 ATTCGCATTGCGA
1 ATTCGCATTGCGA
209143 ATTAGGAAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
40 13 0.27
41 35 0.73
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.38
Consensus pattern (40 bp):
ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACCT
Found at i:210235 original size:17 final size:18
Alignment explanation
Indices: 210215--210249 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
210205 AAAACGATAT
210215 AAAAT-ATAAAATTTAAA
1 AAAATAATAAAATTTAAA
*
210232 AAAATAATAAATTTTAAA
1 AAAATAATAAAATTTAAA
210250 GATTCGTTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
AAAATAATAAAATTTAAA
Found at i:212813 original size:28 final size:28
Alignment explanation
Indices: 212728--212819 Score: 80
Period size: 28 Copynumber: 3.3 Consensus size: 28
212718 CTTTTCATTT
* *
212728 TAATTTGTAAAAAATATAGGTATTATTG
1 TAATTTATAAAAATTATAGGTATTATTG
* * * ** *
212756 TAATTT-GAAAAATGCAGACCTTTTCA-TG
1 TAATTTATAAAAAT-TATAGGTATT-ATTG
212784 TAATTTATAAAAATTATAGGTATTATTG
1 TAATTTATAAAAATTATAGGTATTATTG
212812 TAATTTAT
1 TAATTTAT
212820 GAGAAGTTTT
Statistics
Matches: 47, Mismatches: 13, Indels: 8
0.69 0.19 0.12
Matches are distributed among these distances:
27 6 0.13
28 34 0.72
29 7 0.15
ACGTcount: A:0.40, C:0.04, G:0.12, T:0.43
Consensus pattern (28 bp):
TAATTTATAAAAATTATAGGTATTATTG
Found at i:212869 original size:29 final size:28
Alignment explanation
Indices: 212782--212884 Score: 93
Period size: 29 Copynumber: 3.6 Consensus size: 28
212772 GACCTTTTCA
* *
212782 TGTAATTTATAAAAATTATAGGTA-TTAT
1 TGTAATTTATAAAAGTT-TTGGTATTTAT
* * *
212810 TGTAATTTATGAGAAGTTTT-TTCTTTGAT
1 TGTAATTTAT-AAAAGTTTTGGTATTT-AT
212839 TGTAATTTATAAATAGTTTTGGTATTTAT
1 TGTAATTTATAAA-AGTTTTGGTATTTAT
*
212868 TGTAATATTAAAAAAGT
1 TGTAAT-TTATAAAAGT
212885 GACTTTTATT
Statistics
Matches: 60, Mismatches: 9, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
27 1 0.02
28 15 0.25
29 34 0.57
30 10 0.17
ACGTcount: A:0.36, C:0.01, G:0.14, T:0.50
Consensus pattern (28 bp):
TGTAATTTATAAAAGTTTTGGTATTTAT
Found at i:212969 original size:15 final size:15
Alignment explanation
Indices: 212928--212962 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
212918 TTTTATTGTA
212928 ATTTT-ATAATTTTT
1 ATTTTAATAATTTTT
212942 ATTTTAATAATTTTT
1 ATTTTAATAATTTTT
212957 ATTTTA
1 ATTTTA
212963 GAAATTTACA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 5 0.25
15 15 0.75
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
ATTTTAATAATTTTT
Found at i:215018 original size:25 final size:25
Alignment explanation
Indices: 214990--215039 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
214980 TTTGACCAAA
214990 TCAGCCGCCCCATTTGCCATTTTTT
1 TCAGCCGCCCCATTTGCCATTTTTT
215015 TCAGCCGCCCCATTTGCCATTTTTT
1 TCAGCCGCCCCATTTGCCATTTTTT
215040 GACTTTCAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.12, C:0.36, G:0.12, T:0.40
Consensus pattern (25 bp):
TCAGCCGCCCCATTTGCCATTTTTT
Found at i:219673 original size:30 final size:26
Alignment explanation
Indices: 219615--219664 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
219605 TGACCAAATT
219615 AACCGCCCCATTTGCCATTTTTTTTC
1 AACCGCCCCATTTGCCATTTTTTTTC
219641 AACCGCCCCATTTGCCATTTTTTT
1 AACCGCCCCATTTGCCATTTTTTT
219665 ACTTTCAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.16, C:0.34, G:0.08, T:0.42
Consensus pattern (26 bp):
AACCGCCCCATTTGCCATTTTTTTTC
Found at i:221326 original size:67 final size:67
Alignment explanation
Indices: 221218--221352 Score: 270
Period size: 67 Copynumber: 2.0 Consensus size: 67
221208 ATCTTTGTCG
221218 AAAAGTTGTTTCGGCACGGTTCCTTTAAACTCGTTGAACCTCAAATCCAAGAACTTGAGCGAAGG
1 AAAAGTTGTTTCGGCACGGTTCCTTTAAACTCGTTGAACCTCAAATCCAAGAACTTGAGCGAAGG
221283 CA
66 CA
221285 AAAAGTTGTTTCGGCACGGTTCCTTTAAACTCGTTGAACCTCAAATCCAAGAACTTGAGCGAAGG
1 AAAAGTTGTTTCGGCACGGTTCCTTTAAACTCGTTGAACCTCAAATCCAAGAACTTGAGCGAAGG
221350 CA
66 CA
221352 A
1 A
221353 CTCGAGAATT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 68 1.00
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.25
Consensus pattern (67 bp):
AAAAGTTGTTTCGGCACGGTTCCTTTAAACTCGTTGAACCTCAAATCCAAGAACTTGAGCGAAGG
CA
Found at i:221826 original size:11 final size:11
Alignment explanation
Indices: 221810--221836 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
221800 GTGCATAAAT
221810 GTGCACTTTCG
1 GTGCACTTTCG
221821 GTGCACTTTCG
1 GTGCACTTTCG
221832 GTGCA
1 GTGCA
221837 TCCCATGTTT
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:0.11, C:0.26, G:0.30, T:0.33
Consensus pattern (11 bp):
GTGCACTTTCG
Found at i:230623 original size:2 final size:2
Alignment explanation
Indices: 230616--230648 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
230606 CATCCAGTCC
230616 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
230649 TCAATTTAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:234528 original size:31 final size:31
Alignment explanation
Indices: 234490--234588 Score: 137
Period size: 31 Copynumber: 3.2 Consensus size: 31
234480 TGATGACTAC
*
234490 ATCTTAATTAAATAAAAATGAAAATGATCAT
1 ATCTTAATTAAATAAAAATGAAAATGACCAT
234521 ATCTTAATTAAATAAAAAT-AAAATTGACCAT
1 ATCTTAATTAAATAAAAATGAAAA-TGACCAT
* * * *
234552 ATATTAATTAAATAAAAACGAAAGTGACCAC
1 ATCTTAATTAAATAAAAATGAAAATGACCAT
234583 ATCTTA
1 ATCTTA
234589 TGTTTTTTTA
Statistics
Matches: 60, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
30 4 0.07
31 53 0.88
32 3 0.05
ACGTcount: A:0.54, C:0.10, G:0.06, T:0.30
Consensus pattern (31 bp):
ATCTTAATTAAATAAAAATGAAAATGACCAT
Found at i:234703 original size:26 final size:27
Alignment explanation
Indices: 234674--234743 Score: 65
Period size: 29 Copynumber: 2.6 Consensus size: 27
234664 AAATATAAAA
234674 AAATAAAAATTAAATTACTAAAAT-TT
1 AAATAAAAATTAAATTACTAAAATATT
* * *
234700 AAATATACATATTAAAAATACTAAACTATT
1 AAATA-A-AAATT-AAATTACTAAAATATT
234730 --ATAAAAATTAAATT
1 AAATAAAAATTAAATT
234744 TTTTGAATAT
Statistics
Matches: 35, Mismatches: 5, Indels: 9
0.71 0.10 0.18
Matches are distributed among these distances:
25 4 0.11
26 9 0.26
27 2 0.06
28 7 0.20
29 11 0.31
30 2 0.06
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (27 bp):
AAATAAAAATTAAATTACTAAAATATT
Found at i:235030 original size:25 final size:24
Alignment explanation
Indices: 234992--235056 Score: 67
Period size: 25 Copynumber: 2.6 Consensus size: 24
234982 TTATTATTAG
*
234992 ATTAATCGAGACTTACGAAATTTAA
1 ATTAATCGAAACTTAC-AAATTTAA
* *
235017 ATTAGTCGAAACTTACAAATTTTAT
1 ATTAATCGAAACTTACAAA-TTTAA
* *
235042 AGTAATCAAAACTTA
1 ATTAATCGAAACTTA
235057 TTGTTTTTAT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
24 3 0.09
25 30 0.91
ACGTcount: A:0.45, C:0.12, G:0.09, T:0.34
Consensus pattern (24 bp):
ATTAATCGAAACTTACAAATTTAA
Found at i:235418 original size:7 final size:7
Alignment explanation
Indices: 235406--235444 Score: 51
Period size: 7 Copynumber: 5.4 Consensus size: 7
235396 TTTTCAGTAA
235406 TTTAATT
1 TTTAATT
235413 TTTAATT
1 TTTAATT
235420 TTTATATT
1 TTTA-ATT
* *
235428 TTTTATA
1 TTTAATT
235435 TTTAATT
1 TTTAATT
235442 TTT
1 TTT
235445 TTGAATGTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 21 0.78
8 6 0.22
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (7 bp):
TTTAATT
Found at i:237083 original size:25 final size:28
Alignment explanation
Indices: 237041--237095 Score: 80
Period size: 26 Copynumber: 2.1 Consensus size: 28
237031 GCGTGGGATA
237041 TTTTCTAAAATGA-GTTTTAAGTTTTTT
1 TTTTCTAAAATGATGTTTTAAGTTTTTT
*
237068 TTTTC-AAAAT-ATTTTTTAAGTTTTTT
1 TTTTCTAAAATGATGTTTTAAGTTTTTT
237094 TT
1 TT
237096 AAAGAAAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 1 0.04
26 20 0.77
27 5 0.19
ACGTcount: A:0.25, C:0.04, G:0.07, T:0.64
Consensus pattern (28 bp):
TTTTCTAAAATGATGTTTTAAGTTTTTT
Found at i:237468 original size:27 final size:28
Alignment explanation
Indices: 237410--237492 Score: 159
Period size: 27 Copynumber: 3.0 Consensus size: 28
237400 ATAAGAATGA
237410 TACATCCATGATAAACATTGACATCAAT
1 TACATCCATGATAAACATTGACATCAAT
237438 TACATCCATGATAAACATT-ACATCAAT
1 TACATCCATGATAAACATTGACATCAAT
237465 TACATCCATGATAAACATTGACATCAAT
1 TACATCCATGATAAACATTGACATCAAT
237493 CCCTTCTACA
Statistics
Matches: 54, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
27 27 0.50
28 27 0.50
ACGTcount: A:0.43, C:0.22, G:0.06, T:0.29
Consensus pattern (28 bp):
TACATCCATGATAAACATTGACATCAAT
Found at i:243700 original size:2 final size:2
Alignment explanation
Indices: 243693--243728 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
243683 TAAGCAAATA
243693 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
243729 TACTTCATAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:246057 original size:14 final size:14
Alignment explanation
Indices: 246021--246061 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
246011 ATTTTTTGTC
*
246021 TATATGCAGAGATT
1 TATATGCAGGGATT
*
246035 TATACGCAGGGATT
1 TATATGCAGGGATT
*
246049 TATTTGCAGGGAT
1 TATATGCAGGGAT
246062 AACTTCCCAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.29, C:0.10, G:0.27, T:0.34
Consensus pattern (14 bp):
TATATGCAGGGATT
Found at i:250605 original size:11 final size:13
Alignment explanation
Indices: 250589--250628 Score: 50
Period size: 11 Copynumber: 3.3 Consensus size: 13
250579 ATGTTAAGTT
250589 TATTAATATAAT-
1 TATTAATATAATA
*
250601 T-TTAAGATAATA
1 TATTAATATAATA
250613 TATTAATAT-ATA
1 TATTAATATAATA
250625 TATT
1 TATT
250629 TATTAAACAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 9 0.38
12 9 0.38
13 6 0.25
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (13 bp):
TATTAATATAATA
Found at i:252371 original size:3 final size:3
Alignment explanation
Indices: 252365--252406 Score: 61
Period size: 3 Copynumber: 14.7 Consensus size: 3
252355 ATAATTAATT
*
252365 TAA TAA TAT TAA TAA T-A TAA TAA TAA TAA TAA TAA TAA -AA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
252407 GTGAAAAATT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 4 0.11
3 31 0.89
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:252376 original size:9 final size:9
Alignment explanation
Indices: 252360--252398 Score: 55
Period size: 9 Copynumber: 4.6 Consensus size: 9
252350 TGGTAATAAT
252360 TAAT-TTAA
1 TAATATTAA
252368 TAATATTAA
1 TAATATTAA
252377 TAATA-TAA
1 TAATATTAA
*
252385 TAATAATAA
1 TAATATTAA
252394 TAATA
1 TAATA
252399 ATAAAATAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
8 12 0.41
9 17 0.59
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (9 bp):
TAATATTAA
Found at i:252385 original size:17 final size:17
Alignment explanation
Indices: 252353--252398 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 17
252343 TAGGGTTTGG
*
252353 TAATAATTAATTTAATAA
1 TAATAA-TAATATAATAA
*
252371 TATTAATAATATAATAA
1 TAATAATAATATAATAA
252388 TAATAATAATA
1 TAATAATAATA
252399 ATAAAATAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
17 20 0.80
18 5 0.20
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TAATAATAATATAATAA
Found at i:252390 original size:20 final size:20
Alignment explanation
Indices: 252365--252406 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
252355 ATAATTAATT
* *
252365 TAATAATATTAATAATATAA
1 TAATAATAATAATAATAAAA
252385 TAATAATAATAATAATAAAA
1 TAATAATAATAATAATAAAA
252405 TA
1 TA
252407 GTGAAAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
TAATAATAATAATAATAAAA
Found at i:252680 original size:45 final size:45
Alignment explanation
Indices: 252616--253290 Score: 1091
Period size: 45 Copynumber: 14.9 Consensus size: 45
252606 AAAGCTCCCA
* * *
252616 AAGGTTTTAAAAACATCATGAACTGAAGGGCTTACAGATGACCCG
1 AAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCG
*
252661 AAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCG
1 AAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCG
*
252706 AAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCG
1 AAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCG
*
252751 AAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCTG
1 AAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCG
* *
252796 AAGGTTTTTGATAACATCATGCACTGAAGGGCTTACAGATGACCCG
1 AAGG-TTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCG
* *
252842 AAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACACG
1 AAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCG
* *
252887 GAGGTTTTGAAAACATCATGCACTGAAGGACTTACAAATGACCCG
1 AAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCG
* *
252932 AAGGTTTTGAAAACATCATGCACTGAAAGACTTACAGATGACTCG
1 AAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCG
252977 AAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCG
1 AAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCG
*
253022 AAGATTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCG
1 AAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCG
*
253067 AAGGTTTTTGATAACATCATGCACTGAAGGACTTACAGATGACCCG
1 AAGG-TTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCG
*
253113 AAGGTTTTTGATAACATCATGCACTGAAGGACTTACAGATGACCC-
1 AAGG-TTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCG
* **
253158 ATAGGTTTTGAAAACATCATGCATTGATCGACTTACAGATGACCCG
1 A-AGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCG
* *
253204 AAGGTTTTTGATAACATCATGCACTGAAGGACTTACAGATGACCTG
1 AAGG-TTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCG
253250 AAGGTTTTGAAAAACATCATGCACTGAAGGACTTACAGATG
1 AAGGTTTTG-AAAACATCATGCACTGAAGGACTTACAGATG
253291 TTGGAAATAG
Statistics
Matches: 592, Mismatches: 32, Indels: 11
0.93 0.05 0.02
Matches are distributed among these distances:
45 391 0.66
46 201 0.34
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.24
Consensus pattern (45 bp):
AAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCG
Found at i:253969 original size:22 final size:22
Alignment explanation
Indices: 253944--254029 Score: 90
Period size: 22 Copynumber: 3.9 Consensus size: 22
253934 AAATCCAATA
*
253944 AATCTTTCATCTTTGAAAAGAG
1 AATCTATCATCTTTGAAAAGAG
253966 AATCTATCATCTTT--AAAGAG
1 AATCTATCATCTTTGAAAAGAG
253986 ATAGGT-TATCATCTTTGAAGAA-AG
1 A-A--TCTATCATCTTTGAA-AAGAG
*
254010 AGTCTATCATCTTTGAAAAG
1 AATCTATCATCTTTGAAAAG
254030 TGTAGATGTA
Statistics
Matches: 54, Mismatches: 2, Indels: 16
0.75 0.03 0.22
Matches are distributed among these distances:
20 7 0.13
21 4 0.07
22 36 0.67
23 1 0.02
24 4 0.07
25 2 0.04
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (22 bp):
AATCTATCATCTTTGAAAAGAG
Found at i:255086 original size:75 final size:75
Alignment explanation
Indices: 254962--255135 Score: 240
Period size: 75 Copynumber: 2.3 Consensus size: 75
254952 TGATATAGGG
* * * * *
254962 TTTCAGCATACCCCAACATTTGCTAATACAAACGTTCAAAATGCGTCAACATTCCTCATTCTGAT
1 TTTCAGCATGCCCCAACATTTGCTAATACAAACATTCAAAATACATCAACATTCATCATTCTGAT
255027 TGAAAGGGGC
66 TGAAAGGGGC
* * * * *
255037 TTTCAGCATGCCCCAGCATTTGCTGATATAAATATTCAAAATACATCAACATTCATGATTCTGAT
1 TTTCAGCATGCCCCAACATTTGCTAATACAAACATTCAAAATACATCAACATTCATCATTCTGAT
*
255102 TGAGAGGGGC
66 TGAAAGGGGC
*
255112 TTTCAGTATGCCCCAACATTTGCT
1 TTTCAGCATGCCCCAACATTTGCT
255136 TCTTGTTAAT
Statistics
Matches: 86, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
75 86 1.00
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.30
Consensus pattern (75 bp):
TTTCAGCATGCCCCAACATTTGCTAATACAAACATTCAAAATACATCAACATTCATCATTCTGAT
TGAAAGGGGC
Found at i:256103 original size:21 final size:20
Alignment explanation
Indices: 256055--256108 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
256045 TTGGAGCGTG
*
256055 GGGGGGAATCGGTACCCCCT
1 GGGGGGAATCGGTACCCACT
*
256075 GAGGGGAATCGGTACCCACT
1 GGGGGGAATCGGTACCCACT
256095 AGGGGGGAATCGGT
1 -GGGGGGAATCGGT
256109 TCCCTCCGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 18 0.60
21 12 0.40
ACGTcount: A:0.20, C:0.22, G:0.43, T:0.15
Consensus pattern (20 bp):
GGGGGGAATCGGTACCCACT
Found at i:261726 original size:22 final size:21
Alignment explanation
Indices: 261684--261723 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
261674 GAGTTTATTT
*
261684 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
261705 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
261724 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:269116 original size:12 final size:13
Alignment explanation
Indices: 269093--269121 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
269083 AAAATGAAAA
269093 AAATGCAAAATGT
1 AAATGCAAAATGT
269106 AAATG-AAAATGT
1 AAATGCAAAATGT
269118 AAAT
1 AAAT
269122 ATGTGAATGC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.59, C:0.03, G:0.14, T:0.24
Consensus pattern (13 bp):
AAATGCAAAATGT
Found at i:269125 original size:20 final size:19
Alignment explanation
Indices: 269092--269130 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
269082 AAAAATGAAA
269092 AAAATGCAAAATGTAAATG
1 AAAATGCAAAATGTAAATG
* *
269111 AAAATGTAAATATGTGAATG
1 AAAATGCAAA-ATGTAAATG
269131 CAACAATAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.54, C:0.03, G:0.18, T:0.26
Consensus pattern (19 bp):
AAAATGCAAAATGTAAATG
Found at i:272555 original size:11 final size:13
Alignment explanation
Indices: 272539--272579 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 13
272529 ATGTTAAGTT
272539 TATTAATATAAT-
1 TATTAATATAATA
*
272551 T-TTAAGATAATA
1 TATTAATATAATA
272563 TATTAATATATATA
1 TATTAATATA-ATA
272577 TAT
1 TAT
272580 ATTTTATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 9 0.38
12 2 0.08
13 7 0.29
14 6 0.25
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (13 bp):
TATTAATATAATA
Found at i:274351 original size:3 final size:3
Alignment explanation
Indices: 274321--274363 Score: 54
Period size: 3 Copynumber: 14.7 Consensus size: 3
274311 ATATTTAATT
*
274321 TAA TAA TAT TAA TAA -AA T-A TATA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TA
274364 TAGTGAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
2 4 0.11
3 28 0.80
4 3 0.09
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:274635 original size:45 final size:45
Alignment explanation
Indices: 274571--275158 Score: 935
Period size: 45 Copynumber: 13.0 Consensus size: 45
274561 TTAAAAATCT
* *
274571 CCCGAAGGTTTTAAAAACATCATGCACTGAAGGGCTTACAGATGA
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
*
274616 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
* * *
274661 CCCGAAGGTTTTGAAAACATCATGCACTGATGGGCTTACAGAAGA
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
274706 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
* * *
274751 CCTGAAGGTTTTTGATAACATCATGCACTGAAGGGCTTACAGATGA
1 CCCGAAGG-TTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
* * *
274797 CCCTAAGGTTTTGAAAACATCATACACTGAAGGGCTTACAGATGA
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
* * *
274842 CCCGGAGGTTTTGAAAACATCATGCACTGAATGACTTACAAATGA
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
*
274887 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATAA
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
*
274932 ACCGAAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
*
274977 CCTGAAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
*
275022 CCCGAAGGTTTTTGATAACATCATGCACTGAAGGACTTACAGATGA
1 CCCGAAGG-TTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
* *
275068 CCCGAAGGTCTTTGATAACATCATGCAATGAAGGACTTACAGATGA
1 CCCGAAGGT-TTTGAAAACATCATGCACTGAAGGACTTACAGATGA
*
275114 CCC-AGAGGTTTTGAAAACATCATGCACTGAAGGACTTACAAATGA
1 CCCGA-AGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
275159 TATTCGAATA
Statistics
Matches: 506, Mismatches: 33, Indels: 8
0.93 0.06 0.01
Matches are distributed among these distances:
45 379 0.75
46 127 0.25
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.24
Consensus pattern (45 bp):
CCCGAAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
Found at i:275063 original size:271 final size:272
Alignment explanation
Indices: 274571--275158 Score: 989
Period size: 271 Copynumber: 2.2 Consensus size: 272
274561 TTAAAAATCT
* * * *
274571 CCCGAAGGTTTTAAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACAT
1 CCCGGAGGTTTTGAAAACATCATGCACTGAAGGACTTACAAATGACCCGAAGGTTTTGAAAACAT
* * * * *
274636 CATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGATGGGCTTACA
66 CATGCACTGAAGGACTTACAGATAAACCGAAGGTTTTGAAAACATCATGCACTGAAGGACTTACA
*
274701 GAAGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCTGAAGGTTTTTGA
131 GAAGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTTGA
* * *
274766 TAACATCATGCACTGAAGGGCTTACAGATGACCCTAAGGT-TTTGAAAACATCATACACTGAAGG
196 TAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTCTTTGAAAACATCATACAATGAAGG
*
274830 GCTTACAGATGA
261 ACTTACAGATGA
*
274842 CCCGGAGGTTTTGAAAACATCATGCACTGAATGACTTACAAATGACCCGAAGGTTTTGAAAACAT
1 CCCGGAGGTTTTGAAAACATCATGCACTGAAGGACTTACAAATGACCCGAAGGTTTTGAAAACAT
274907 CATGCACTGAAGGACTTACAGATAAACCGAAGGTTTTGAAAACATCATGCACTGAAGGACTTACA
66 CATGCACTGAAGGACTTACAGATAAACCGAAGGTTTTGAAAACATCATGCACTGAAGGACTTACA
* *
274972 GATGACCTGAAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTTGA
131 GAAGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTTGA
* *
275037 TAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTCTTTGATAACATCATGCAATGAAGG
196 TAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTCTTTGAAAACATCATACAATGAAGG
275102 ACTTACAGATGA
261 ACTTACAGATGA
*
275114 CCCAGAGGTTTTGAAAACATCATGCACTGAAGGACTTACAAATGA
1 CCCGGAGGTTTTGAAAACATCATGCACTGAAGGACTTACAAATGA
275159 TATTCGAATA
Statistics
Matches: 295, Mismatches: 21, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
271 220 0.75
272 75 0.25
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.24
Consensus pattern (272 bp):
CCCGGAGGTTTTGAAAACATCATGCACTGAAGGACTTACAAATGACCCGAAGGTTTTGAAAACAT
CATGCACTGAAGGACTTACAGATAAACCGAAGGTTTTGAAAACATCATGCACTGAAGGACTTACA
GAAGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTTGA
TAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTCTTTGAAAACATCATACAATGAAGG
ACTTACAGATGA
Found at i:277549 original size:21 final size:23
Alignment explanation
Indices: 277518--277578 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
277508 CAGAATCCCC
* *
277518 AGGGGGTATCGATTCCCC-T-GA
1 AGGGGGAATCGATTCCCCTTCAA
* *
277539 GGGGGGAATCGGTTCCCCTTCAA
1 AGGGGGAATCGATTCCCCTTCAA
277562 AGGGGGAATCGATTCCC
1 AGGGGGAATCGATTCCC
277579 TCTGCACAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
21 15 0.47
22 1 0.03
23 16 0.50
ACGTcount: A:0.20, C:0.25, G:0.34, T:0.21
Consensus pattern (23 bp):
AGGGGGAATCGATTCCCCTTCAA
Found at i:286330 original size:11 final size:13
Alignment explanation
Indices: 286314--286353 Score: 50
Period size: 11 Copynumber: 3.3 Consensus size: 13
286304 ATGTTAAGTT
286314 TATTAATATAAT-
1 TATTAATATAATA
*
286326 T-TTAAGATAATA
1 TATTAATATAATA
286338 TATTAATAT-ATA
1 TATTAATATAATA
286350 TATT
1 TATT
286354 TTATTAAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 9 0.38
12 9 0.38
13 6 0.25
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (13 bp):
TATTAATATAATA
Found at i:286644 original size:2 final size:2
Alignment explanation
Indices: 286637--286695 Score: 52
Period size: 2 Copynumber: 30.5 Consensus size: 2
286627 AAATATTATT
* * * *
286637 TA TA TA TA TA TA TA TA TA -A GA CT- TA GA TA AA TA T- TA TT TA
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA
286677 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
286696 TGACAACGAT
Statistics
Matches: 46, Mismatches: 7, Indels: 8
0.75 0.11 0.13
Matches are distributed among these distances:
1 3 0.07
2 43 0.93
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:287889 original size:20 final size:20
Alignment explanation
Indices: 287864--287902 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
287854 CAAGTGAGAG
287864 ATTATTAGTTGTCATGCAAA
1 ATTATTAGTTGTCATGCAAA
287884 ATTATTAGTTGTCATGCAA
1 ATTATTAGTTGTCATGCAA
287903 CTAATAATAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.10, G:0.15, T:0.41
Consensus pattern (20 bp):
ATTATTAGTTGTCATGCAAA
Found at i:287928 original size:21 final size:20
Alignment explanation
Indices: 287904--287945 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
287894 GTCATGCAAC
*
287904 TAATAATAGTTGTATAATGCA
1 TAATAATAGTT-CATAATGCA
*
287925 TAATAATGGTTCATAATGCA
1 TAATAATAGTTCATAATGCA
287945 T
1 T
287946 TGTAAGTTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.40, C:0.07, G:0.14, T:0.38
Consensus pattern (20 bp):
TAATAATAGTTCATAATGCA
Found at i:288906 original size:95 final size:95
Alignment explanation
Indices: 288731--288953 Score: 293
Period size: 95 Copynumber: 2.3 Consensus size: 95
288721 ATCGTCTAGC
** * * *
288731 TGTAAGAGCATTTGCAACTGCCAAAGAAAGGTATAAGAGTGACTGCATATGAAACATATAAGAAT
1 TGTAAGAGCATTTGCAGTTGCCAATGGAAGGTATAAGAGTGACTGCATATGAAACATATAACAAT
* * *
288796 TTAACGCATACATCCTTCATTCAGTTTAGT
66 TCAACACACACATCCTTCATTCAGTTTAGT
* * * * *
288826 TGTAAGATCATTTGCAGTTTCCAATGGAAGGTTTAAGAGTGACTGTATGTGAAACATATAACAAT
1 TGTAAGAGCATTTGCAGTTGCCAATGGAAGGTATAAGAGTGACTGCATATGAAACATATAACAAT
* *
288891 TCAATACACATATCCTTCATTCAGTTTAGT
66 TCAACACACACATCCTTCATTCAGTTTAGT
* *
288921 TGTAGGAGCATTTGCGGTTGCCAATGGAAGGTA
1 TGTAAGAGCATTTGCAGTTGCCAATGGAAGGTA
288954 CAAGCCAGGG
Statistics
Matches: 108, Mismatches: 20, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
95 108 1.00
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.31
Consensus pattern (95 bp):
TGTAAGAGCATTTGCAGTTGCCAATGGAAGGTATAAGAGTGACTGCATATGAAACATATAACAAT
TCAACACACACATCCTTCATTCAGTTTAGT
Found at i:295205 original size:5 final size:5
Alignment explanation
Indices: 295088--295196 Score: 159
Period size: 5 Copynumber: 21.2 Consensus size: 5
295078 AGACTAAATC
295088 TTATA TTATA TTATA TTATA TTATA TTATATA TTATA TTATA TTATTTA
1 TTATA TTATA TTATA TTATA TTATA -T-TATA TTATA TTATA TTA--TA
295137 TTATA TTATA -T-TA TTATA TTATA TTTATA TTATA TTATA TTATA TTATA
1 TTATA TTATA TTATA TTATA TTATA -TTATA TTATA TTATA TTATA TTATA
295186 TTATA TTATA T
1 TTATA TTATA T
295197 ATTATATTAA
Statistics
Matches: 97, Mismatches: 0, Indels: 14
0.87 0.00 0.13
Matches are distributed among these distances:
3 2 0.02
4 2 0.02
5 77 0.79
6 7 0.07
7 9 0.09
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TTATA
Found at i:295729 original size:2 final size:2
Alignment explanation
Indices: 295722--295748 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
295712 AAGCTTAGAG
295722 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 T
295749 CAAATTAGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:296996 original size:10 final size:10
Alignment explanation
Indices: 296983--297016 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
296973 AAATTATTTT
296983 AAAAATTAAA
1 AAAAATTAAA
296993 AAAAATTAAA
1 AAAAATTAAA
*
297003 AAAAAATAAA
1 AAAAATTAAA
297013 AAAA
1 AAAA
297017 TAATGAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (10 bp):
AAAAATTAAA
Found at i:300220 original size:21 final size:22
Alignment explanation
Indices: 300184--300224 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
300174 AATCATTAAA
*
300184 ATAATTGAATTTAAATTATTCG
1 ATAATTGAAATTAAATTATTCG
300206 ATAATT-AAATTAAATTATT
1 ATAATTGAAATTAAATTATT
300225 ATTTTTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.46
Consensus pattern (22 bp):
ATAATTGAAATTAAATTATTCG
Found at i:300265 original size:3 final size:3
Alignment explanation
Indices: 300257--300286 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
300247 TTTGTTCTCT
300257 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
300287 ACTGCAACTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:303780 original size:65 final size:65
Alignment explanation
Indices: 303650--303779 Score: 244
Period size: 65 Copynumber: 2.0 Consensus size: 65
303640 AGTTGAACCC
303650 TGTATATCAGGGCCAAAGAGGTTTGTCTTTTCTGCCATTTTTTGTCTGGCAATTGGCTTCATTTT
1 TGTATATCAGGGCCAAAGAGGTTTGTCTTTTCTGCCATTTTTTGTCTGGCAATTGGCTTCATTTT
*
303715 TGTATATCAGGGCCAAAGAGGTTTGTCTTTTCTGCCA-TTTTTGTCTGGCAATTGGCTTCTTTTT
1 TGTATATCAGGGCCAAAGAGGTTTGTCTTTTCTGCCATTTTTTGTCTGGCAATTGGCTTCATTTT
303779 T
1 T
303780 TAATTTTAAA
Statistics
Matches: 64, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
64 27 0.42
65 37 0.58
ACGTcount: A:0.16, C:0.17, G:0.22, T:0.45
Consensus pattern (65 bp):
TGTATATCAGGGCCAAAGAGGTTTGTCTTTTCTGCCATTTTTTGTCTGGCAATTGGCTTCATTTT
Found at i:308819 original size:31 final size:28
Alignment explanation
Indices: 308760--308826 Score: 80
Period size: 31 Copynumber: 2.3 Consensus size: 28
308750 ATTAATATAT
* * *
308760 ATATATTATCTTAAATATATTTTTAAAA
1 ATATATTAACTTAAAAATATTTTAAAAA
308788 ATATATTAACTTAAAAAATACTTTTCAAAAA
1 ATATATTAACTT-AAAAATA-TTTT-AAAAA
308819 ATATATTA
1 ATATATTA
308827 CATTTTAAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
28 11 0.33
29 6 0.18
30 4 0.12
31 12 0.36
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (28 bp):
ATATATTAACTTAAAAATATTTTAAAAA
Found at i:309034 original size:29 final size:25
Alignment explanation
Indices: 308973--309034 Score: 70
Period size: 29 Copynumber: 2.3 Consensus size: 25
308963 AAAATAAAAA
*
308973 TAAAATACTTAAATATATTTTAAGT
1 TAAAATATTTAAATATATTTTAAGT
*
308998 TAAGATATTTAAAATATATTTTTAAAAGT
1 TAAAATATTT-AAATATA-TTTT--AAGT
309027 TAAAATAT
1 TAAAATAT
309035 AAAAAATTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
25 8 0.27
26 7 0.23
27 4 0.13
29 11 0.37
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.44
Consensus pattern (25 bp):
TAAAATATTTAAATATATTTTAAGT
Found at i:309040 original size:29 final size:26
Alignment explanation
Indices: 308983--309041 Score: 64
Period size: 29 Copynumber: 2.2 Consensus size: 26
308973 TAAAATACTT
* **
308983 AAATATATTTTAAGTTAAGATATTTA
1 AAATATATTTTAAGTTAAAATATAAA
309009 AAATATATTTTTAAAAGTTAAAATATAAA
1 AAATATA-TTTT--AAGTTAAAATATAAA
309038 AAAT
1 AAAT
309042 TATAAATTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 7 0.26
27 4 0.15
29 16 0.59
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (26 bp):
AAATATATTTTAAGTTAAAATATAAA
Found at i:315018 original size:15 final size:15
Alignment explanation
Indices: 314998--315029 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
314988 AACAAGGTTT
314998 CCTAGCATTGAGCAG
1 CCTAGCATTGAGCAG
315013 CCTAGCATTGAGCAG
1 CCTAGCATTGAGCAG
315028 CC
1 CC
315030 AGGAGAGGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.25, C:0.31, G:0.25, T:0.19
Consensus pattern (15 bp):
CCTAGCATTGAGCAG
Found at i:317496 original size:60 final size:60
Alignment explanation
Indices: 317403--317523 Score: 242
Period size: 60 Copynumber: 2.0 Consensus size: 60
317393 AAAAAAACTA
317403 AGGGTCTGTTTGTTTAGCTGTAATTGGTTTTCCAGAAAATGAATTACTGGAATTTGAATT
1 AGGGTCTGTTTGTTTAGCTGTAATTGGTTTTCCAGAAAATGAATTACTGGAATTTGAATT
317463 AGGGTCTGTTTGTTTAGCTGTAATTGGTTTTCCAGAAAATGAATTACTGGAATTTGAATT
1 AGGGTCTGTTTGTTTAGCTGTAATTGGTTTTCCAGAAAATGAATTACTGGAATTTGAATT
317523 A
1 A
317524 CTGGAATTTG
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 61 1.00
ACGTcount: A:0.27, C:0.08, G:0.23, T:0.41
Consensus pattern (60 bp):
AGGGTCTGTTTGTTTAGCTGTAATTGGTTTTCCAGAAAATGAATTACTGGAATTTGAATT
Found at i:317522 original size:15 final size:15
Alignment explanation
Indices: 317502--317583 Score: 121
Period size: 15 Copynumber: 5.5 Consensus size: 15
317492 TTCCAGAAAA
317502 TGAATTACTGGAATT
1 TGAATTACTGGAATT
317517 TGAATTACTGGAATT
1 TGAATTACTGGAATT
**
317532 TGAATTACTGGAAAA
1 TGAATTACTGGAATT
317547 TGAATTACTGGAATT
1 TGAATTACTGGAATT
**
317562 TGAATT-CTGGAAAA
1 TGAATTACTGGAATT
317576 TGAATTAC
1 TGAATTAC
317584 ATCTCTGTAA
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
14 12 0.20
15 48 0.80
ACGTcount: A:0.38, C:0.07, G:0.20, T:0.35
Consensus pattern (15 bp):
TGAATTACTGGAATT
Found at i:317536 original size:30 final size:30
Alignment explanation
Indices: 317502--317583 Score: 139
Period size: 30 Copynumber: 2.8 Consensus size: 30
317492 TTCCAGAAAA
**
317502 TGAATTACTGGAATTTGAATTACTGGAATT
1 TGAATTACTGGAAAATGAATTACTGGAATT
317532 TGAATTACTGGAAAATGAATTACTGGAATT
1 TGAATTACTGGAAAATGAATTACTGGAATT
317562 TGAATT-CTGGAAAATGAATTAC
1 TGAATTACTGGAAAATGAATTAC
317584 ATCTCTGTAA
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 16 0.32
30 34 0.68
ACGTcount: A:0.38, C:0.07, G:0.20, T:0.35
Consensus pattern (30 bp):
TGAATTACTGGAAAATGAATTACTGGAATT
Found at i:317546 original size:45 final size:44
Alignment explanation
Indices: 317497--317583 Score: 147
Period size: 45 Copynumber: 2.0 Consensus size: 44
317487 TGGTTTTCCA
**
317497 GAAAATGAATTACTGGAATTTGAATTACTGGAATTTGAATTACTG
1 GAAAATGAATTACTGGAATTTGAATT-CTGGAAAATGAATTACTG
317542 GAAAATGAATTACTGGAATTTGAATTCTGGAAAATGAATTAC
1 GAAAATGAATTACTGGAATTTGAATTCTGGAAAATGAATTAC
317584 ATCTCTGTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
44 14 0.35
45 26 0.65
ACGTcount: A:0.40, C:0.07, G:0.20, T:0.33
Consensus pattern (44 bp):
GAAAATGAATTACTGGAATTTGAATTCTGGAAAATGAATTACTG
Found at i:317590 original size:20 final size:20
Alignment explanation
Indices: 317566--317635 Score: 122
Period size: 20 Copynumber: 3.5 Consensus size: 20
317556 GGAATTTGAA
317566 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
* *
317586 CTCTGTAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
317606 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
317626 TTCTGGAAAA
1 TTCTGGAAAA
317636 CATCTGAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.34
Consensus pattern (20 bp):
TTCTGGAAAATGAATTACAT
Found at i:317850 original size:27 final size:26
Alignment explanation
Indices: 317799--317869 Score: 81
Period size: 27 Copynumber: 2.6 Consensus size: 26
317789 TTTACTAAAA
* *
317799 TATTATTGAAATATA-AATAATATTAT
1 TATTATT-AAATATATAAAAAAATTAT
317825 TCATTATTAAATATATAAAAAAATTAT
1 T-ATTATTAAATATATAAAAAAATTAT
317852 TATATATTATAATATATA
1 TAT-TATTA-AATATATA
317870 TCTTATATTA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
26 10 0.26
27 21 0.54
28 8 0.21
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (26 bp):
TATTATTAAATATATAAAAAAATTAT
Found at i:317884 original size:27 final size:26
Alignment explanation
Indices: 317849--317932 Score: 81
Period size: 24 Copynumber: 3.4 Consensus size: 26
317839 ATAAAAAAAT
317849 TATTA-TATATTATAATATATATCTTA
1 TATTATTATATTATAATATATAT-TTA
*
317875 TATTATTATAATATAATGAT-TATTT-
1 TATTATTATATTATAAT-ATATATTTA
* *
317900 TA-TATAATATTAAAATA-ATA-TTA
1 TATTATTATATTATAATATATATTTA
317923 TATTATTATA
1 TATTATTATA
317933 AAATATAAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
22 2 0.04
23 5 0.10
24 17 0.35
25 2 0.04
26 7 0.15
27 13 0.27
28 2 0.04
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (26 bp):
TATTATTATATTATAATATATATTTA
Found at i:317933 original size:27 final size:29
Alignment explanation
Indices: 317849--317933 Score: 81
Period size: 29 Copynumber: 3.0 Consensus size: 29
317839 ATAAAAAAAT
* *
317849 TATTATATATTATAATA-TATA-TCTTATAT
1 TATTATA-A-TATAATATTATATTATTATAA
*
317878 TATTATAATATAATGATTATTTTA-TATAA
1 TATTATAATATAAT-ATTATATTATTATAA
317907 TATTA-AA-ATAATATTATATTATTATAA
1 TATTATAATATAATATTATATTATTATAA
317934 AATATAAATA
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
26 8 0.17
27 16 0.33
28 4 0.08
29 19 0.40
30 1 0.02
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (29 bp):
TATTATAATATAATATTATATTATTATAA
Found at i:318203 original size:42 final size:41
Alignment explanation
Indices: 318144--318256 Score: 199
Period size: 42 Copynumber: 2.7 Consensus size: 41
318134 ATGAATTACA
*
318144 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACGTT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAAC-AT
318186 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACAT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACAT
318227 TTCCGGAAAAACGAATTACGTGAAACAAAC
1 TTCCGG-AAAACGAATTACGTGAAACAAAC
318257 CCTGGAATTC
Statistics
Matches: 69, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
41 7 0.10
42 62 0.90
ACGTcount: A:0.45, C:0.19, G:0.19, T:0.16
Consensus pattern (41 bp):
TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACAT
Found at i:318347 original size:14 final size:15
Alignment explanation
Indices: 318314--318375 Score: 74
Period size: 14 Copynumber: 4.3 Consensus size: 15
318304 AAACAGACCC
**
318314 TTACTGGAATTTGAA
1 TTACTGGAAAATGAA
318329 TTACTGGAAAATG-A
1 TTACTGGAAAATGAA
**
318343 TTACTGGAATTTGAA
1 TTACTGGAAAATGAA
318358 TT-CTGGAAAATGAA
1 TTACTGGAAAATGAA
318372 TTAC
1 TTAC
318376 ATTTATGTAA
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
14 24 0.62
15 15 0.38
ACGTcount: A:0.37, C:0.08, G:0.19, T:0.35
Consensus pattern (15 bp):
TTACTGGAAAATGAA
Found at i:318356 original size:29 final size:29
Alignment explanation
Indices: 318314--318375 Score: 108
Period size: 29 Copynumber: 2.1 Consensus size: 29
318304 AAACAGACCC
318314 TTACTGGAATTTGAATTACTGGAAAATG-A
1 TTACTGGAATTTGAATT-CTGGAAAATGAA
318343 TTACTGGAATTTGAATTCTGGAAAATGAA
1 TTACTGGAATTTGAATTCTGGAAAATGAA
318372 TTAC
1 TTAC
318376 ATTTATGTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
28 10 0.31
29 22 0.69
ACGTcount: A:0.37, C:0.08, G:0.19, T:0.35
Consensus pattern (29 bp):
TTACTGGAATTTGAATTCTGGAAAATGAA
Found at i:318419 original size:19 final size:20
Alignment explanation
Indices: 318358--318425 Score: 104
Period size: 19 Copynumber: 3.5 Consensus size: 20
318348 GGAATTTGAA
318358 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
* *
318378 TTATGTAAAATGAA-TACAT
1 TTCTGGAAAATGAATTACAT
318397 TTCTGGAAAATGAATTACA-
1 TTCTGGAAAATGAATTACAT
318416 TTCTGGAAAA
1 TTCTGGAAAA
318426 CATCTGAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
19 27 0.63
20 16 0.37
ACGTcount: A:0.43, C:0.09, G:0.15, T:0.34
Consensus pattern (20 bp):
TTCTGGAAAATGAATTACAT
Found at i:318653 original size:29 final size:28
Alignment explanation
Indices: 318590--318657 Score: 75
Period size: 29 Copynumber: 2.4 Consensus size: 28
318580 CTTTACTAAA
* * *
318590 ATATTATTGAAATATATAAATAATATTAT
1 ATATTATT-AAATATAAAAAAAATAGTAT
318619 -TCATTATTAAATATAAAAAAAATTAGTAT
1 AT-ATTATTAAATATAAAAAAAA-TAGTAT
318648 ATATTATTAA
1 ATATTATTAA
318658 TAAATAATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
28 13 0.39
29 19 0.58
30 1 0.03
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.43
Consensus pattern (28 bp):
ATATTATTAAATATAAAAAAAATAGTAT
Found at i:318695 original size:23 final size:23
Alignment explanation
Indices: 318647--318707 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 23
318637 AAAATTAGTA
*
318647 TATATTATTAATAA-ATAATATCT
1 TATATTATT-ATAATATAATATAT
318670 TATATTATTATAATATAAT-TGAT
1 TATATTATTATAATATAATAT-AT
*
318693 TATTTTA-TATAATAT
1 TATATTATTATAATAT
318708 TAAAAATATA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
22 13 0.38
23 21 0.62
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (23 bp):
TATATTATTATAATATAATATAT
Found at i:318725 original size:22 final size:23
Alignment explanation
Indices: 318700--318743 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
318690 GATTATTTTA
318700 TATAATATTAAAAATA-TAATAT
1 TATAATATTAAAAATATTAATAT
* *
318722 TATATTATTATAAATATTAATA
1 TATAATATTAAAAATATTAATA
318744 AATATATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TATAATATTAAAAATATTAATAT
Found at i:318744 original size:26 final size:26
Alignment explanation
Indices: 318590--318768 Score: 76
Period size: 26 Copynumber: 6.9 Consensus size: 26
318580 CTTTACTAAA
*
318590 ATATTATTGA-AATATATAAATAATATT
1 ATATTATT-ATAA-ATATTAATAATATT
* * * *
318617 AT-TCATTATTAAATATAAAAAAAATT
1 ATATTATTA-TAAATATTAATAATATT
*
318643 AGTATATATTATTAATA--AATAATATCTT
1 A-TAT-TATTATAAATATTAATAATA--TT
* * *
318671 ATATTATTATAATATAATTGATTATTTT
1 ATATTATTATAA-AT-ATTAATAATATT
318699 ATATAATATTA-AAA-A-T-ATAATATT
1 ATAT--TATTATAAATATTAATAATATT
318723 ATATTATTATAAATATTAATAA-A-T
1 ATATTATTATAAATATTAATAATATT
*
318747 ATATT-TTA-AATATTTTAATAAT
1 ATATTATTATAA-ATATTAATAAT
318769 TAATATTTTG
Statistics
Matches: 119, Mismatches: 14, Indels: 41
0.68 0.08 0.24
Matches are distributed among these distances:
22 7 0.06
23 15 0.13
24 17 0.14
25 4 0.03
26 34 0.29
27 10 0.08
28 17 0.14
29 6 0.05
30 9 0.08
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.47
Consensus pattern (26 bp):
ATATTATTATAAATATTAATAATATT
Found at i:318748 original size:22 final size:22
Alignment explanation
Indices: 318704--318760 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
318694 ATTTTATATA
* *
318704 ATATTAAAAATA-TAATATTAT
1 ATATTATAAATATTAATATAAT
318725 ATTATTATAAATATTAATA-AAT
1 A-TATTATAAATATTAATATAAT
*
318747 ATATTTTAAATATT
1 ATATTATAAATATT
318761 TTAATAATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
21 13 0.42
22 13 0.42
23 5 0.16
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
ATATTATAAATATTAATATAAT
Found at i:318759 original size:52 final size:53
Alignment explanation
Indices: 318605--318774 Score: 145
Period size: 52 Copynumber: 3.2 Consensus size: 53
318595 ATTGAAATAT
* ** * *
318605 ATAAATAATATTATT-CATTATTA-AATATAA-AAAAAATTAGTATATATTATTA
1 ATAAATAATA-TATTATATTATTATAATATAATAAATTATT-TTATATAATATTA
* **
318657 ATAAATAATATCTTATATTATTATAATATAATTGATTATTTTATATAATATTA
1 ATAAATAATATATTATATTATTATAATATAATAAATTATTTTATATAATATTA
* *
318710 A-AAAT-ATAATATTATATTATTATAAATATTAATAAATATATTTTAAAT-ATTTTA
1 ATAAATAAT-ATATTATATTATTAT-AATA-TAATAAAT-TATTTTATATAATATTA
*
318764 ATAATTAATAT
1 ATAAATAATAT
318775 TTTGATGAAA
Statistics
Matches: 95, Mismatches: 14, Indels: 15
0.77 0.11 0.12
Matches are distributed among these distances:
51 5 0.05
52 35 0.37
53 23 0.24
54 16 0.17
55 14 0.15
56 2 0.02
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (53 bp):
ATAAATAATATATTATATTATTATAATATAATAAATTATTTTATATAATATTA
Found at i:318865 original size:15 final size:15
Alignment explanation
Indices: 318845--318926 Score: 112
Period size: 15 Copynumber: 5.5 Consensus size: 15
318835 TTCCAGAAAA
318845 TGAATTACTGGAATT
1 TGAATTACTGGAATT
*
318860 TGAATTACTGAAATT
1 TGAATTACTGGAATT
**
318875 TGAATTACTGGAAAA
1 TGAATTACTGGAATT
318890 TGAATTACTGGAATT
1 TGAATTACTGGAATT
**
318905 TGAATT-CTGGAAAA
1 TGAATTACTGGAATT
318919 TGAATTAC
1 TGAATTAC
318927 ATTTCTGTAA
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
14 12 0.21
15 46 0.79
ACGTcount: A:0.39, C:0.07, G:0.18, T:0.35
Consensus pattern (15 bp):
TGAATTACTGGAATT
Found at i:318881 original size:30 final size:30
Alignment explanation
Indices: 318845--318926 Score: 130
Period size: 30 Copynumber: 2.8 Consensus size: 30
318835 TTCCAGAAAA
**
318845 TGAATTACTGGAATTTGAATTACTGAAATT
1 TGAATTACTGGAAAATGAATTACTGAAATT
*
318875 TGAATTACTGGAAAATGAATTACTGGAATT
1 TGAATTACTGGAAAATGAATTACTGAAATT
318905 TGAATT-CTGGAAAATGAATTAC
1 TGAATTACTGGAAAATGAATTAC
318927 ATTTCTGTAA
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 16 0.33
30 33 0.67
ACGTcount: A:0.39, C:0.07, G:0.18, T:0.35
Consensus pattern (30 bp):
TGAATTACTGGAAAATGAATTACTGAAATT
Found at i:318891 original size:45 final size:44
Alignment explanation
Indices: 318840--318926 Score: 140
Period size: 45 Copynumber: 2.0 Consensus size: 44
318830 TGGTTTTCCA
*
318840 GAAAATGAATTACTGGAATTTGAATTACT-GAAATTTGAATTACTG
1 GAAAATGAATTACTGGAATTTGAATT-CTGGAAA-ATGAATTACTG
318885 GAAAATGAATTACTGGAATTTGAATTCTGGAAAATGAATTAC
1 GAAAATGAATTACTGGAATTTGAATTCTGGAAAATGAATTAC
318927 ATTTCTGTAA
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
44 10 0.25
45 30 0.75
ACGTcount: A:0.41, C:0.07, G:0.18, T:0.33
Consensus pattern (44 bp):
GAAAATGAATTACTGGAATTTGAATTCTGGAAAATGAATTACTG
Found at i:318932 original size:20 final size:20
Alignment explanation
Indices: 318909--318978 Score: 131
Period size: 20 Copynumber: 3.5 Consensus size: 20
318899 GGAATTTGAA
318909 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
*
318929 TTCTGTAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
318949 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
318969 TTCTGGAAAA
1 TTCTGGAAAA
318979 CATCTTAAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (20 bp):
TTCTGGAAAATGAATTACAT
Found at i:319102 original size:22 final size:22
Alignment explanation
Indices: 319058--319119 Score: 54
Period size: 22 Copynumber: 2.7 Consensus size: 22
319048 AAAATTTATA
*
319058 AATTATTAATTATTAAAGTAATAGT
1 AATTAGTAATT-TTAAA--AATAGT
* *
319083 ACTTA-TATATTTTAAAAATATT
1 AATTAGTA-ATTTTAAAAATAGT
319105 AATTAGTAATTTTAA
1 AATTAGTAATTTTAA
319120 TATCTTACTA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
22 16 0.50
23 2 0.06
24 7 0.22
25 7 0.22
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.47
Consensus pattern (22 bp):
AATTAGTAATTTTAAAAATAGT
Found at i:319186 original size:28 final size:27
Alignment explanation
Indices: 319132--319196 Score: 71
Period size: 28 Copynumber: 2.4 Consensus size: 27
319122 TCTTACTAAA
* *
319132 ATATTATTGAAATATAAATAATATTAT
1 ATATTATTAAAATATAAAAAATATTAT
319159 -TCATTATTAAATATATAAAAAA-ATTTAT
1 AT-ATTATTAAA-ATATAAAAAATA-TTAT
319187 ATATTATTAA
1 ATATTATTAA
319197 TAAATAATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
26 1 0.03
27 9 0.28
28 21 0.66
29 1 0.03
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (27 bp):
ATATTATTAAAATATAAAAAATATTAT
Found at i:319200 original size:23 final size:25
Alignment explanation
Indices: 319173--319223 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
319163 TATTAAATAT
319173 ATAAA-AAAAT-TTATA-TATTATTA
1 ATAAATAAAATCTTATATTATTA-TA
*
319196 ATAAATAATATCTTATATTATTATA
1 ATAAATAAAATCTTATATTATTATA
319221 ATA
1 ATA
319224 TAATTGATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
23 5 0.21
24 4 0.17
25 10 0.42
26 5 0.21
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (25 bp):
ATAAATAAAATCTTATATTATTATA
Found at i:319234 original size:23 final size:23
Alignment explanation
Indices: 319186--319262 Score: 63
Period size: 23 Copynumber: 3.3 Consensus size: 23
319176 AAAAAATTTA
*
319186 TATATTATTAATAA-ATAATATCT
1 TATATTATT-ATAATATAATATAT
319209 TATATTATTATAATATAAT-TGAT
1 TATATTATTATAATATAATAT-AT
*
319232 TAT-TT-TCTATAATATTAAAATAT
1 TATATTAT-TATAATA-TAATATAT
*
319255 AATATTAT
1 TATATTAT
319263 ATTATAAATA
Statistics
Matches: 44, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
21 1 0.02
22 14 0.32
23 25 0.57
24 3 0.07
25 1 0.02
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.51
Consensus pattern (23 bp):
TATATTATTATAATATAATATAT
Found at i:319286 original size:21 final size:20
Alignment explanation
Indices: 319243--319295 Score: 65
Period size: 21 Copynumber: 2.7 Consensus size: 20
319233 ATTTTCTATA
*
319243 ATATTA-AAATA-TAATATT
1 ATATTATAAATATTAATAAT
319261 ATATTATAAATATTAATAAAT
1 ATATTATAAATATTAAT-AAT
*
319282 ATATTTTAAATATT
1 ATATTATAAATATT
319296 TTAATAATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
18 6 0.20
19 5 0.17
20 4 0.13
21 15 0.50
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
ATATTATAAATATTAATAAT
Found at i:319287 original size:51 final size:52
Alignment explanation
Indices: 319145--319310 Score: 143
Period size: 51 Copynumber: 3.2 Consensus size: 52
319135 TTATTGAAAT
*
319145 ATAAATAATATTATTCATTATTAAATATATAA-AAA-A-A-TTTATATATTATTA
1 ATAAATAATATTA-T-ATTATTAAATAT-TAATAAATATATTTTATATAATATTA
** *
319196 ATAAATAATATCTTATATTATTATAATA-TAATTGAT-TATTTTCTATAATATTA
1 ATAAATAATA--TTATATTATTA-AATATTAATAAATATATTTTATATAATATTA
* *
319249 A-AATATAATATTATATTA-TAAATATTAATAAATATATTTTAAAT-ATTTTA
1 ATAA-ATAATATTATATTATTAAATATTAATAAATATATTTTATATAATATTA
*
319299 ATAATTAATATT
1 ATAAATAATATT
319311 TTGATGAAAA
Statistics
Matches: 94, Mismatches: 10, Indels: 23
0.74 0.08 0.18
Matches are distributed among these distances:
49 4 0.04
50 24 0.26
51 36 0.38
52 8 0.09
53 22 0.23
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.48
Consensus pattern (52 bp):
ATAAATAATATTATATTATTAAATATTAATAAATATATTTTATATAATATTA
Found at i:319319 original size:535 final size:547
Alignment explanation
Indices: 318314--319341 Score: 1829
Period size: 535 Copynumber: 1.9 Consensus size: 547
318304 AAACAGACCC
*
318314 TTACTGGAATTTGAATTACTGGAAAATGATTACTGGAATTTGAATTCTGGAAAATGAATTACATT
1 TTACTGAAATTTGAATTACTGGAAAATGATTACTGGAATTTGAATTCTGGAAAATGAATTACATT
*
318379 TATGTAAAATGAATACATTTCTGGAAAATGAATTACATTCTGGAAAACATCTGAAAAACGTTTTA
66 TATGTAAAATGAATACATTTCTGGAAAATGAATTACATTCTGGAAAACATCTAAAAAACGTTTTA
318444 TGATGTTTGGAAGATGTTATTTAAACATTTTTTCGGTATATTTTAGTGAAATAAAATTTTATAAA
131 TGATGTTTGGAAGATGTTATTTAAACATTTTTTCGG-ATATTTTAGTGAAATAAAATTTTATAAA
318509 TTATATTAATTATTATTAAAGTAATAGTACTATATCATATTTTAAAAATATTAATTAGTATATTT
195 TTATATTAA-TATTATTAAAGTAATAGTACTATATCATATTTTAAAAATATTAATTAGTATATTT
318574 TAATATCTTTACTAAAATATTATTGAAATATATAAATAATATTATTCATTATTAAATATAAAAAA
259 TAATATCTTTACTAAAATATTATTGAAATATATAAATAATATTATTCATTATTAAATATAAAAAA
318639 AATTAGTATATATTATTAATAAATAATATCTTATATTATTATAATATAATTGATTATTTTATATA
324 AATTA-TATATATTATTAATAAATAATATCTTATATTATTATAATATAATTGATTATTTTATATA
318704 ATATTAAAAATATAATATTATATTATTATAAATATTAATAAATATATTTTAAATATTTTAATAAT
388 ATATTAAAAATATAATATTATATTATTATAAATATTAATAAATATATTTTAAATATTTTAATAAT
318769 TAATATTTTGATGAAAATGATATTAAAATATTTTATTAGGGTCTGTTTGTTTAGCTGTAATTGGT
453 TAATATTTTGATGAAAATGATATTAAAATATTTTATTAGGGTCTGTTTGTTTAGCTGTAATTGGT
318834 TTTCCAGAAAATGAATTACTGGAATTTGAA
518 TTTCCAGAAAATGAATTACTGGAATTTGAA
318864 TTACTGAAATTTGAATTACTGGAAAATGAATTACTGGAATTTGAATTCTGGAAAATGAATTACAT
1 TTACTGAAATTTGAATTACTGGAAAATG-ATTACTGGAATTTGAATTCTGGAAAATGAATTACAT
*
318929 TTCTGTAAAATGAATTACATTTCTGGAAAATGAATTACATTTCTGGAAAACATCTTAAAAAACGT
65 TTATGTAAAATGAA-TACATTTCTGGAAAATGAATTACA-TTCTGGAAAACATC-TAAAAAACGT
318994 TTTATGATGTTTGGAAGATGTTATTTAAACATTTTTTCGG-TATTTTAGTGAAATAAAA-TTTAT
127 TTTATGATGTTTGGAAGATGTTATTTAAACATTTTTTCGGATATTTTAGTGAAATAAAATTTTAT
319057 AAA-T-TATT-A-ATTATTAAAGTAATAGTACT-TAT-ATATTTTAAAAATATTAATTAGTA-AT
192 AAATTATATTAATATTATTAAAGTAATAGTACTATATCATATTTTAAAAATATTAATTAGTATAT
319115 TTTAATATC-TTACTAAAATATTATTG-AA-ATATAAATAATATTATTCATTATTAAATATATAA
257 TTTAATATCTTTACTAAAATATTATTGAAATATATAAATAATATTATTCATTATTAAATATA-AA
*
319177 AAAAATT-TATATATTATTAATAAATAATATCTTATATTATTATAATATAATTGATTATTTTCTA
321 AAAAATTATATATATTATTAATAAATAATATCTTATATTATTATAATATAATTGATTATTTTATA
319241 TAATATT-AAAATATAATA-T-TA-TATTATAAATATTAATAAATATATTTTAAATATTTTAATA
386 TAATATTAAAAATATAATATTATATTATTATAAATATTAATAAATATATTTTAAATATTTTAATA
319302 ATTAATATTTTGATGAAAATGATATTAAAATATTTTATTA
451 ATTAATATTTTGATGAAAATGATATTAAAATATTTTATTA
319342 ATATTAAATT
Statistics
Matches: 469, Mismatches: 4, Indels: 25
0.94 0.01 0.05
Matches are distributed among these distances:
535 80 0.17
536 2 0.00
537 1 0.00
538 11 0.02
539 63 0.13
540 31 0.07
541 11 0.02
542 17 0.04
543 11 0.02
544 24 0.05
545 3 0.01
546 20 0.04
548 1 0.00
549 4 0.01
550 28 0.06
551 57 0.12
552 42 0.09
553 14 0.03
554 49 0.10
ACGTcount: A:0.43, C:0.04, G:0.09, T:0.44
Consensus pattern (547 bp):
TTACTGAAATTTGAATTACTGGAAAATGATTACTGGAATTTGAATTCTGGAAAATGAATTACATT
TATGTAAAATGAATACATTTCTGGAAAATGAATTACATTCTGGAAAACATCTAAAAAACGTTTTA
TGATGTTTGGAAGATGTTATTTAAACATTTTTTCGGATATTTTAGTGAAATAAAATTTTATAAAT
TATATTAATATTATTAAAGTAATAGTACTATATCATATTTTAAAAATATTAATTAGTATATTTTA
ATATCTTTACTAAAATATTATTGAAATATATAAATAATATTATTCATTATTAAATATAAAAAAAA
TTATATATATTATTAATAAATAATATCTTATATTATTATAATATAATTGATTATTTTATATAATA
TTAAAAATATAATATTATATTATTATAAATATTAATAAATATATTTTAAATATTTTAATAATTAA
TATTTTGATGAAAATGATATTAAAATATTTTATTAGGGTCTGTTTGTTTAGCTGTAATTGGTTTT
CCAGAAAATGAATTACTGGAATTTGAA
Found at i:319588 original size:42 final size:43
Alignment explanation
Indices: 319481--319602 Score: 210
Period size: 43 Copynumber: 2.9 Consensus size: 43
319471 ATGAATTACA
*
319481 TTCCGGGAAAACGAATTACGTGAAACAAACACGGGAAAACGTT
1 TTCCGGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
319524 TTCCGGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
1 TTCCGGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
* *
319567 TTCC-GGAAAACGAATTACGTGAAACATACACTGGAA
1 TTCCGGGAAAACGAATTACGTGAAACAAACACGGGAA
319603 TTCGGGGAAA
Statistics
Matches: 76, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
42 30 0.39
43 46 0.61
ACGTcount: A:0.43, C:0.19, G:0.21, T:0.17
Consensus pattern (43 bp):
TTCCGGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
Found at i:319712 original size:14 final size:15
Alignment explanation
Indices: 319654--319716 Score: 83
Period size: 15 Copynumber: 4.3 Consensus size: 15
319644 AAACAGACCC
**
319654 TTACTGGAATTTGAA
1 TTACTGGAAAATGAA
319669 TTACTGGAAAATGAA
1 TTACTGGAAAATGAA
**
319684 TTACTGGAATTTGAA
1 TTACTGGAAAATGAA
319699 TT-CTGGAAAATGAA
1 TTACTGGAAAATGAA
319713 TTAC
1 TTAC
319717 ATTTCTGTAA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
14 12 0.29
15 29 0.71
ACGTcount: A:0.38, C:0.08, G:0.19, T:0.35
Consensus pattern (15 bp):
TTACTGGAAAATGAA
Found at i:319714 original size:29 final size:30
Alignment explanation
Indices: 319654--319716 Score: 119
Period size: 30 Copynumber: 2.1 Consensus size: 30
319644 AAACAGACCC
319654 TTACTGGAATTTGAATTACTGGAAAATGAA
1 TTACTGGAATTTGAATTACTGGAAAATGAA
319684 TTACTGGAATTTGAATT-CTGGAAAATGAA
1 TTACTGGAATTTGAATTACTGGAAAATGAA
319713 TTAC
1 TTAC
319717 ATTTCTGTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 16 0.48
30 17 0.52
ACGTcount: A:0.38, C:0.08, G:0.19, T:0.35
Consensus pattern (30 bp):
TTACTGGAATTTGAATTACTGGAAAATGAA
Found at i:319722 original size:20 final size:20
Alignment explanation
Indices: 319699--319768 Score: 131
Period size: 20 Copynumber: 3.5 Consensus size: 20
319689 GGAATTTGAA
319699 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
*
319719 TTCTGTAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
319739 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
319759 TTCTGGAAAA
1 TTCTGGAAAA
319769 CATCTGAAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (20 bp):
TTCTGGAAAATGAATTACAT
Found at i:320067 original size:20 final size:20
Alignment explanation
Indices: 320042--320080 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
320032 TTGATTATTT
320042 TATATAATATTAAAAATATA
1 TATATAATATTAAAAATATA
* *
320062 TATATATTATTATAAATAT
1 TATATAATATTAAAAATAT
320081 TAATAAATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
TATATAATATTAAAAATATA
Found at i:320101 original size:32 final size:29
Alignment explanation
Indices: 320037--320109 Score: 87
Period size: 30 Copynumber: 2.4 Consensus size: 29
320027 TATAATTGAT
*
320037 TATTTTATATAATATTAAAAATATATATA
1 TATTTTATATAATATTAAAAATATATAAA
320066 TATTATTATA-AATATTAATAAATATATTTAAA
1 TATT-TTATATAATATTAA-AAATATA--TAAA
320098 TATTTTA-ATAAT
1 TATTTTATATAAT
320110 TAATATTTTG
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
29 12 0.32
30 13 0.34
31 6 0.16
32 7 0.18
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (29 bp):
TATTTTATATAATATTAAAAATATATAAA
Found at i:320349 original size:42 final size:42
Alignment explanation
Indices: 320290--320409 Score: 222
Period size: 42 Copynumber: 2.9 Consensus size: 42
320280 ATGAATTACA
*
320290 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACGTT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
320332 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
*
320374 TTCCGGAAAACGAATTACGTGAAACAAACACTGGAA
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAA
320410 TTCGGGGAAA
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 76 1.00
ACGTcount: A:0.44, C:0.19, G:0.20, T:0.17
Consensus pattern (42 bp):
TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
Found at i:320518 original size:14 final size:15
Alignment explanation
Indices: 320460--320522 Score: 83
Period size: 15 Copynumber: 4.3 Consensus size: 15
320450 AAACAGACCC
**
320460 TTACTGGAATTTGAA
1 TTACTGGAAAATGAA
320475 TTACTGGAAAATGAA
1 TTACTGGAAAATGAA
**
320490 TTACTGGAATTTGAA
1 TTACTGGAAAATGAA
320505 TT-CTGGAAAATGAA
1 TTACTGGAAAATGAA
320519 TTAC
1 TTAC
320523 ATTTCTGTAA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
14 12 0.29
15 29 0.71
ACGTcount: A:0.38, C:0.08, G:0.19, T:0.35
Consensus pattern (15 bp):
TTACTGGAAAATGAA
Found at i:320520 original size:29 final size:30
Alignment explanation
Indices: 320460--320522 Score: 119
Period size: 30 Copynumber: 2.1 Consensus size: 30
320450 AAACAGACCC
320460 TTACTGGAATTTGAATTACTGGAAAATGAA
1 TTACTGGAATTTGAATTACTGGAAAATGAA
320490 TTACTGGAATTTGAATT-CTGGAAAATGAA
1 TTACTGGAATTTGAATTACTGGAAAATGAA
320519 TTAC
1 TTAC
320523 ATTTCTGTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 16 0.48
30 17 0.52
ACGTcount: A:0.38, C:0.08, G:0.19, T:0.35
Consensus pattern (30 bp):
TTACTGGAATTTGAATTACTGGAAAATGAA
Found at i:320528 original size:20 final size:20
Alignment explanation
Indices: 320505--320574 Score: 131
Period size: 20 Copynumber: 3.5 Consensus size: 20
320495 GGAATTTGAA
320505 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
*
320525 TTCTGTAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
320545 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
320565 TTCTGGAAAA
1 TTCTGGAAAA
320575 CATCTGAAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (20 bp):
TTCTGGAAAATGAATTACAT
Found at i:320838 original size:23 final size:23
Alignment explanation
Indices: 320790--320850 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 23
320780 AAAATTATTA
*
320790 TATATTATTAATAA-ATAATATCT
1 TATATTATT-ATAATATAATATAT
320813 TATATTATTATAATATAAT-TGAT
1 TATATTATTATAATATAATAT-AT
*
320836 TATTTTA-TATAATAT
1 TATATTATTATAATAT
320851 TAAAAATATA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
22 13 0.38
23 21 0.62
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (23 bp):
TATATTATTATAATATAATATAT
Found at i:320868 original size:22 final size:23
Alignment explanation
Indices: 320843--320886 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
320833 GATTATTTTA
320843 TATAATATTAAAAATA-TAATAT
1 TATAATATTAAAAATATTAATAT
* *
320865 TATATTATTATAAATATTAATA
1 TATAATATTAAAAATATTAATA
320887 AATATATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TATAATATTAAAAATATTAATAT
Found at i:320891 original size:22 final size:22
Alignment explanation
Indices: 320847--320903 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
320837 ATTTTATATA
* *
320847 ATATTAAAAATA-TAATATTAT
1 ATATTATAAATATTAATATAAT
320868 ATTATTATAAATATTAATA-AAT
1 A-TATTATAAATATTAATATAAT
*
320890 ATATTTTAAATATT
1 ATATTATAAATATT
320904 TTAATAATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
21 13 0.42
22 13 0.42
23 5 0.16
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
ATATTATAAATATTAATATAAT
Found at i:320902 original size:52 final size:53
Alignment explanation
Indices: 320744--320917 Score: 142
Period size: 55 Copynumber: 3.2 Consensus size: 53
320734 ATATTATTGA
* * ** *
320744 AATATATAA-ATATTATTCATTATTA-AATATATAAAAAAAATTATTATATATTATT
1 AATAAATAATATATTA-T-ATTATTATAATATA-ATAAATTATT-TTATATAATATT
* **
320799 AATAAATAATATCTTATATTATTATAATATAATTGATTATTTTATATAATATT
1 AATAAATAATATATTATATTATTATAATATAATAAATTATTTTATATAATATT
* *
320852 AA-AAAT-ATAATATTATATTATTATAAATATTAATAAATATATTTTAAAT-ATTTT
1 AATAAATAAT-ATATTATATTATTAT-AATA-TAATAAAT-TATTTTATATAATATT
*
320906 AATAATTAATAT
1 AATAAATAATAT
320918 TTTGATGAAA
Statistics
Matches: 97, Mismatches: 14, Indels: 16
0.76 0.11 0.13
Matches are distributed among these distances:
51 2 0.02
52 18 0.19
53 17 0.18
54 24 0.25
55 29 0.30
56 7 0.07
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.48
Consensus pattern (53 bp):
AATAAATAATATATTATATTATTATAATATAATAAATTATTTTATATAATATT
Found at i:321127 original size:802 final size:802
Alignment explanation
Indices: 318864--321264 Score: 4432
Period size: 802 Copynumber: 3.0 Consensus size: 802
318854 GGAATTTGAA
*
318864 TTACTGAAATTTGAATTACTGGAAAATGAATTACTGGAATTTGAATTCTGGAAAATGAATTACAT
1 TTACTGGAATTTGAATTACTGGAAAATGAATTACTGGAATTTGAATTCTGGAAAATGAATTACAT
*
318929 TTCTGTAAAATGAATTACATTTCTGGAAAATGAATTACATTTCTGGAAAACATCTTAAAAAACGT
66 TTCTGTAAAATGAATTACATTTCTGGAAAATGAATTACATTTCTGGAAAACATC-TGAAAAACGT
318994 TTTATGATGTTTGGAAGATGTTATTTAAACATTTTTTCGG--TATTTTAGTGAAATAAAA-TTTA
130 TTTATGATGTTTGGAAGATGTTATTTAAACATTTTTTCGGTATATTTTAGTGAAATAAAATTTTA
319056 TAAA-T-TATTAATTATTAAAGTAATAGTACT-TATATATTTTAAAAATATTAATTAGTA-ATTT
195 TAAATTATATTAATTATTAAAGTAATAGTACTATATATATTTTAAAAATATTAATTAGTATATTT
*
319117 TAATATC-TTACTAAAATATTATTGAAATATAAATAATATTATTCATTATTAAATATAT-AAAAA
260 TAATATCTTTACTAAAATATTATTGAAATATATATAATATTATTCATTATTAAATATATAAAAAA
*
319180 AA-T-TTATATATTATTAATAAATAATATCTTATATTATTATAATATAATTGATTATTTTCTATA
325 AATTATTATATATTATTAATAAATAATATCTTATATTATTATAATATAATTGATTATTTTATATA
319243 ATATT-AAAATATAATAT-TA-TATTATAAATATTAATAAATATATTTTAAATATTTTAATAATT
390 ATATTAAAAATATAATATATATTATTATAAATATTAATAAATATATTTTAAATATTTTAATAATT
319305 AATATTTTGATGAAAATGATATTAAAATATTTTATTAATATTAAATTCATAAAATAAAATTA-TT
455 AATATTTTGATGAAAATGATATTAAAATATTTTATTAATATTAAATTCATAAAATAAAATTATTT
*
319369 TGAGTA-TTTTGCTTTGAAGTGAAAGTTCGGAAAATGACTTACGGAAAATGAATCCGTAAGTCAT
520 TGAGTATTTTTGCTTTGAAGTAAAAGTTCGGAAAATGACTTACGGAAAATGAATCCGTAAGTCAT
319433 TTTACAGAAAACACAAAGGAAATCCTGTTACTAGGAAAATGAATTACATTCCGGGAAAACGAATT
585 TTTACAGAAAACACAAAGGAAATCCTGTTACTAGGAAAATGAATTACATTCC-GGAAAACGAATT
319498 ACGTGAAACAAACACGGGAAAACGTTTTCCGGGAAAACGAATTACGTGAAACAAACACGGGAAAA
649 ACGTGAAACAAACACGGGAAAACGTTTTCC-GGAAAACGAATTACGTGAAACAAACACGGGAAAA
*
319563 CATTTTCCGGAAAACGAATTACGTGAAACATACACTGGAATTCGGGGAAAAACCAATTCCGTAAT
713 CATTTTCCGGAAAACGAATTACGTGAAACAAACACTGGAATTCGGGG-AAAACCAATTCCGTAAT
319628 TCGAATTACGGGAAACAAACAGACCC
777 TCGAATTACGGGAAACAAACAGACCC
319654 TTACTGGAATTTGAATTACTGGAAAATGAATTACTGGAATTTGAATTCTGGAAAATGAATTACAT
1 TTACTGGAATTTGAATTACTGGAAAATGAATTACTGGAATTTGAATTCTGGAAAATGAATTACAT
319719 TTCTGTAAAATGAATTACATTTCTGGAAAATGAATTACATTTCTGGAAAACATCTGAAAAACGTT
66 TTCTGTAAAATGAATTACATTTCTGGAAAATGAATTACATTTCTGGAAAACATCTGAAAAACGTT
319784 TTATGATGTTTGGAAGATGTTATTTAAACATTTTTTCGGTATATTTTAGTGAAAT-AAATTTTAT
131 TTATGATGTTTGGAAGATGTTATTTAAACATTTTTTCGGTATATTTTAGTGAAATAAAATTTTAT
*
319848 AAATTATATTAATTATTTATTAAAGTAATAGTATTAT-TATATTTTAAAAATATTAATTAGTATA
196 AAATTATATT-A--A-TTATTAAAGTAATAGTACTATATATATTTTAAAAATATTAATTAGTATA
319912 TTTTAATATCTTTACTAAAATATTATTGAAATATATAAATAATATTATTCATTATTAAATATATA
257 TTTTAATATCTTTACTAAAATATTATTGAAATATAT--ATAATATTATTCATTATTAAATATATA
*
319977 AAAAAAATTTATTATATATTTTTAATAAATAATATCTTATATTATTATAATATAATTGATTATTT
320 AAAAAAA-TTATTATATATTATTAATAAATAATATCTTATATTATTATAATATAATTGATTATTT
320042 TATATAATATTAAAAATAT-ATATATATTATTATAAATATTAATAAATATA-TTTAAATATTTTA
384 TATATAATATTAAAAATATAATATATATTATTATAAATATTAATAAATATATTTTAAATATTTTA
320105 ATAATTAATATTTTGATGAAAATGATATTAAAATATTTTATTAATATTAAATTCATAAAATAAAA
449 ATAATTAATATTTTGATGAAAATGATATTAAAATATTTTATTAATATTAAATTCATAAAATAAAA
320170 TTATTTTGAGTATTTTTGCTTTGAAGTGAAAAGTTCGGAAAATGACTTACGGAAAATGAATCCGT
514 TTATTTTGAGTATTTTTGCTTTGAAGT-AAAAGTTCGGAAAATGACTTACGGAAAATGAATCCGT
320235 AAGTCATTTTACAGAAAACACAAAGGAAATCCTGTTACTAGGAAAATGAATTACATTCCGGAAAA
578 AAGTCATTTTACAGAAAACACAAAGGAAATCCTGTTACTAGGAAAATGAATTACATTCCGGAAAA
320300 CGAATTACGTGAAACAAACACGGGAAAACGTTTTCCGGAAAACGAATTACGTGAAACAAACACGG
643 CGAATTACGTGAAACAAACACGGGAAAACGTTTTCCGGAAAACGAATTACGTGAAACAAACACGG
320365 GAAAACATTTTCCGGAAAACGAATTACGTGAAACAAACACTGGAATTCGGGGAAAACCAATTCCG
708 GAAAACATTTTCCGGAAAACGAATTACGTGAAACAAACACTGGAATTCGGGGAAAACCAATTCCG
320430 TAATTCGAATTACGGGAAACAAACAGACCC
773 TAATTCGAATTACGGGAAACAAACAGACCC
320460 TTACTGGAATTTGAATTACTGGAAAATGAATTACTGGAATTTGAATTCTGGAAAATGAATTACAT
1 TTACTGGAATTTGAATTACTGGAAAATGAATTACTGGAATTTGAATTCTGGAAAATGAATTACAT
320525 TTCTGTAAAATGAATTACATTTCTGGAAAATGAATTACATTTCTGGAAAACATCTGAAAAACGTT
66 TTCTGTAAAATGAATTACATTTCTGGAAAATGAATTACATTTCTGGAAAACATCTGAAAAACGTT
320590 TTATGATGTTTGGAAGATGTTATTTAAACATTTTTTCGGTATATTTTAGTGAAATAAAATTTTAT
131 TTATGATGTTTGGAAGATGTTATTTAAACATTTTTTCGGTATATTTTAGTGAAATAAAATTTTAT
320655 AAATTATATTAATTATTAAAGTAATAGTACTATAT-TATTTTAAAAATATTAATTAGTATATTTT
196 AAATTATATTAATTATTAAAGTAATAGTACTATATATATTTTAAAAATATTAATTAGTATATTTT
320719 AATATCTTTACTAAAATATTATTGAAATATATA-AATATTATTCATTATTAAATATATAAAAAAA
261 AATATCTTTACTAAAATATTATTGAAATATATATAATATTATTCATTATTAAATATATAAAAAAA
320783 ATTATTATATATTATTAATAAATAATATCTTATATTATTATAATATAATTGATTATTTTATATAA
326 ATTATTATATATTATTAATAAATAATATCTTATATTATTATAATATAATTGATTATTTTATATAA
320848 TATTAAAAATATAATATTATATTATTATAAATATTAATAAATATATTTTAAATATTTTAATAATT
391 TATTAAAAATATAATA-TATATTATTATAAATATTAATAAATATATTTTAAATATTTTAATAATT
320913 AATATTTTGATGAAAATGATATTAAAATATTTTATTAATATTAAATTCATAAAATAAAATTATTT
455 AATATTTTGATGAAAATGATATTAAAATATTTTATTAATATTAAATTCATAAAATAAAATTATTT
*
320978 TGAGTATTTTTGCTTTGAAGTAAAAAGTTCGGAAAATGACTTACGGAAAATGAATTCGTAAGTCA
520 TGAGTATTTTTGCTTTGAAGT-AAAAGTTCGGAAAATGACTTACGGAAAATGAATCCGTAAGTCA
*
321043 TTTTACAGAAAACACAAAGGAAATCCTGTTACTAGGAAAATGAATTATATTCCGGAAAACGAATT
584 TTTTACAGAAAACACAAAGGAAATCCTGTTACTAGGAAAATGAATTACATTCCGGAAAACGAATT
321108 ACGTGAAACAAACACGGGAAAACGTTTTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAAC
649 ACGTGAAACAAACACGGGAAAACGTTTTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAAC
321173 ATTTTCCGGAAAACGAATTACGTGAAACAAACACTGGAATTCGGGGAAAACCAATTCCGTAATTC
714 ATTTTCCGGAAAACGAATTACGTGAAACAAACACTGGAATTCGGGGAAAACCAATTCCGTAATTC
321238 GAATTACGGGAAACAAACAGACCC
779 GAATTACGGGAAACAAACAGACCC
321262 TTA
1 TTA
321265 ATATTAAATT
Statistics
Matches: 1569, Mismatches: 13, Indels: 46
0.96 0.01 0.03
Matches are distributed among these distances:
789 49 0.03
790 121 0.08
791 22 0.01
792 1 0.00
793 4 0.00
794 1 0.00
796 1 0.00
797 43 0.03
798 12 0.01
799 99 0.06
800 35 0.02
801 55 0.04
802 375 0.24
803 81 0.05
804 3 0.00
805 67 0.04
806 319 0.20
807 130 0.08
808 56 0.04
809 95 0.06
ACGTcount: A:0.43, C:0.09, G:0.12, T:0.36
Consensus pattern (802 bp):
TTACTGGAATTTGAATTACTGGAAAATGAATTACTGGAATTTGAATTCTGGAAAATGAATTACAT
TTCTGTAAAATGAATTACATTTCTGGAAAATGAATTACATTTCTGGAAAACATCTGAAAAACGTT
TTATGATGTTTGGAAGATGTTATTTAAACATTTTTTCGGTATATTTTAGTGAAATAAAATTTTAT
AAATTATATTAATTATTAAAGTAATAGTACTATATATATTTTAAAAATATTAATTAGTATATTTT
AATATCTTTACTAAAATATTATTGAAATATATATAATATTATTCATTATTAAATATATAAAAAAA
ATTATTATATATTATTAATAAATAATATCTTATATTATTATAATATAATTGATTATTTTATATAA
TATTAAAAATATAATATATATTATTATAAATATTAATAAATATATTTTAAATATTTTAATAATTA
ATATTTTGATGAAAATGATATTAAAATATTTTATTAATATTAAATTCATAAAATAAAATTATTTT
GAGTATTTTTGCTTTGAAGTAAAAGTTCGGAAAATGACTTACGGAAAATGAATCCGTAAGTCATT
TTACAGAAAACACAAAGGAAATCCTGTTACTAGGAAAATGAATTACATTCCGGAAAACGAATTAC
GTGAAACAAACACGGGAAAACGTTTTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACAT
TTTCCGGAAAACGAATTACGTGAAACAAACACTGGAATTCGGGGAAAACCAATTCCGTAATTCGA
ATTACGGGAAACAAACAGACCC
Found at i:321151 original size:42 final size:42
Alignment explanation
Indices: 321092--321211 Score: 222
Period size: 42 Copynumber: 2.9 Consensus size: 42
321082 ATGAATTATA
*
321092 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACGTT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
321134 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
*
321176 TTCCGGAAAACGAATTACGTGAAACAAACACTGGAA
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAA
321212 TTCGGGGAAA
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 76 1.00
ACGTcount: A:0.44, C:0.19, G:0.20, T:0.17
Consensus pattern (42 bp):
TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
Done.