Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11
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: 47972186
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2603476 characters in sequence are not A, C, G, or T
File 105 of 145
Found at i:35403814 original size:27 final size:27
Alignment explanation
Indices: 35403784--35403937 Score: 179
Period size: 27 Copynumber: 5.8 Consensus size: 27
35403774 TTTGCCCTAT
35403784 GAGGGTATTTCGATAATTTTACCCTTC
1 GAGGGTATTTCGATAATTTTACCCTTC
*
35403811 GAGGGTATTTCGATAA--TTACCCTTT
1 GAGGGTATTTCGATAATTTTACCCTTC
* * *
35403836 GAGAGCATTTCGGTAATTTTACCCTTC
1 GAGGGTATTTCGATAATTTTACCCTTC
* *
35403863 GAAGGTATTTCGATAATTTTACCTTTC
1 GAGGGTATTTCGATAATTTTACCCTTC
* * * *
35403890 G-GGGTATTTTGGTCATTTTACCCATC
1 GAGGGTATTTCGATAATTTTACCCTTC
* *
35403916 GAGGGTATTTCAATTATTTTAC
1 GAGGGTATTTCGATAATTTTAC
35403938 AACCTTTTCG
Statistics
Matches: 104, Mismatches: 20, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
25 21 0.20
26 20 0.19
27 63 0.61
ACGTcount: A:0.23, C:0.17, G:0.19, T:0.42
Consensus pattern (27 bp):
GAGGGTATTTCGATAATTTTACCCTTC
Found at i:35403923 original size:53 final size:53
Alignment explanation
Indices: 35403790--35403937 Score: 176
Period size: 53 Copynumber: 2.8 Consensus size: 53
35403780 CTATGAGGGT
*
35403790 ATTTCGATAATTTTACCCTTCGAGGGTATTTCGATAA--TTACCCTTTGAGAGC
1 ATTTCGGTAATTTTACCCTTCGAGGGTATTTCGATAATTTTA-CCTTTGAGAGC
* * *
35403842 ATTTCGGTAATTTTACCCTTCGAAGGTATTTCGATAATTTTACCTTTCG-GGGT
1 ATTTCGGTAATTTTACCCTTCGAGGGTATTTCGATAATTTTACCTTT-GAGAGC
* * * * *
35403895 ATTTTGGTCATTTTACCCATCGAGGGTATTTCAATTATTTTAC
1 ATTTCGGTAATTTTACCCTTCGAGGGTATTTCGATAATTTTAC
35403938 AACCTTTTCG
Statistics
Matches: 83, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
52 35 0.42
53 44 0.53
54 4 0.05
ACGTcount: A:0.23, C:0.18, G:0.17, T:0.43
Consensus pattern (53 bp):
ATTTCGGTAATTTTACCCTTCGAGGGTATTTCGATAATTTTACCTTTGAGAGC
Found at i:35412836 original size:18 final size:17
Alignment explanation
Indices: 35412808--35412842 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
35412798 GACAAAGAAT
35412808 CAATAAATACAAATAAG
1 CAATAAATACAAATAAG
*
35412825 CAATACAATACACATAAG
1 CAATA-AATACAAATAAG
35412843 AGCAATAATC
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:0.60, C:0.17, G:0.06, T:0.17
Consensus pattern (17 bp):
CAATAAATACAAATAAG
Found at i:35413250 original size:28 final size:24
Alignment explanation
Indices: 35413199--35413251 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 24
35413189 AATAGGGTCC
*
35413199 TAGAAAATAAATTATATATATGTA
1 TAGAAAATAAATGATATATATGTA
35413223 TAGATAAATAAAATGATATAATAATGTA
1 TAGA-AAAT-AAATGATAT-AT-ATGTA
35413251 T
1 T
35413252 TATATACTCG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
24 4 0.17
25 4 0.17
26 8 0.33
27 2 0.08
28 6 0.25
ACGTcount: A:0.55, C:0.00, G:0.09, T:0.36
Consensus pattern (24 bp):
TAGAAAATAAATGATATATATGTA
Found at i:35413476 original size:14 final size:14
Alignment explanation
Indices: 35413457--35413494 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
35413447 GTGATAATAA
*
35413457 TAATAATCATAAAT
1 TAATAATAATAAAT
*
35413471 TAATAATAATAGAT
1 TAATAATAATAAAT
35413485 TAATAATAAT
1 TAATAATAAT
35413495 GTTACTGAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.37
Consensus pattern (14 bp):
TAATAATAATAAAT
Found at i:35413491 original size:17 final size:16
Alignment explanation
Indices: 35413451--35413494 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
35413441 ATAGCGGTGA
35413451 TAATAATAATAATCAT
1 TAATAATAATAATCAT
* *
35413467 AAATTAATAATAATAGAT
1 TAA-TAATAATAAT-CAT
35413485 TAATAATAAT
1 TAATAATAAT
35413495 GTTACTGAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
16 2 0.09
17 17 0.74
18 4 0.17
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.36
Consensus pattern (16 bp):
TAATAATAATAATCAT
Found at i:35414624 original size:9 final size:8
Alignment explanation
Indices: 35414613--35414660 Score: 51
Period size: 8 Copynumber: 5.8 Consensus size: 8
35414603 AATAGCCTTA
35414613 TTTTTATT
1 TTTTTATT
35414621 ATTTTTATT
1 -TTTTTATT
*
35414630 TTATTATT
1 TTTTTATT
*
35414638 TTTATATT
1 TTTTTATT
35414646 TTGTTTATT
1 TT-TTTATT
*
35414655 TATTTA
1 TTTTTA
35414661 ATTTGGGCCG
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
8 19 0.58
9 14 0.42
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (8 bp):
TTTTTATT
Found at i:35414631 original size:14 final size:14
Alignment explanation
Indices: 35414614--35414642 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
35414604 ATAGCCTTAT
35414614 TTTTATTATTTTTA
1 TTTTATTATTTTTA
35414628 TTTTATTATTTTTA
1 TTTTATTATTTTTA
35414642 T
1 T
35414643 ATTTTGTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTTATTATTTTTA
Found at i:35414652 original size:20 final size:24
Alignment explanation
Indices: 35414610--35414659 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 24
35414600 TTTAATAGCC
*
35414610 TTATTTTTATTATTTTTATTTTA-
1 TTATTTTTATTATTTTTAGTTTAT
35414633 TTATTTTTA-TA-TTTT-GTTTAT
1 TTATTTTTATTATTTTTAGTTTAT
35414654 TTATTT
1 TTATTT
35414660 AATTTGGGCC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 4 0.16
21 10 0.40
22 2 0.08
23 9 0.36
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (24 bp):
TTATTTTTATTATTTTTAGTTTAT
Found at i:35431910 original size:19 final size:19
Alignment explanation
Indices: 35431886--35431922 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
35431876 ATGATGTGTC
35431886 AATAATATAAAAAAATTGA
1 AATAATATAAAAAAATTGA
* *
35431905 AATAATATTAAATAATTG
1 AATAATATAAAAAAATTG
35431923 GTAAGGGATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.32
Consensus pattern (19 bp):
AATAATATAAAAAAATTGA
Found at i:35433316 original size:43 final size:43
Alignment explanation
Indices: 35433250--35433624 Score: 561
Period size: 43 Copynumber: 8.7 Consensus size: 43
35433240 AAAAATAAAC
* * *
35433250 GCCGTTAAAGGTCATGTTCTTTAGCGGCGCTTTTCCCGCAAAT
1 GCCGCTAAAGGCCATGTTCTTTAGCGGCGCTTTTCCCACAAAT
* *
35433293 GCCACTAAAGCCCATGTTCTTTAGCGGCGCTTTTCCCACAAAT
1 GCCGCTAAAGGCCATGTTCTTTAGCGGCGCTTTTCCCACAAAT
* * *
35433336 GCCGCTAAAGGCCATGTTCTTCAGCGGCGCTTTTCCCGCAAAC
1 GCCGCTAAAGGCCATGTTCTTTAGCGGCGCTTTTCCCACAAAT
* *
35433379 GCCGCTAAAGGCCATGTTCTTTAGTGGCGCTTTTCCCAAAAAT
1 GCCGCTAAAGGCCATGTTCTTTAGCGGCGCTTTTCCCACAAAT
* * *
35433422 GCCGCTAAAGGCCATGTTCTTCAGCGGCGCTTTTCCCGCAAAC
1 GCCGCTAAAGGCCATGTTCTTTAGCGGCGCTTTTCCCACAAAT
* *
35433465 GCCGCTAAAGGCCATGTTCTTTAGTGGCGCTTTTCCCAAAAAT
1 GCCGCTAAAGGCCATGTTCTTTAGCGGCGCTTTTCCCACAAAT
* * *
35433508 GCCGCTAAAGGCCATGTTCTTCAGCGGCGCTTTTCCCGCAAAC
1 GCCGCTAAAGGCCATGTTCTTTAGCGGCGCTTTTCCCACAAAT
* *
35433551 GCCGCTAAAGGCCATGTTCTTTAGTGGCGCTTTTCCCAAAAAT
1 GCCGCTAAAGGCCATGTTCTTTAGCGGCGCTTTTCCCACAAAT
*
35433594 GCCGCTAAAGGCCATGTTCTTCAGCGGCGCT
1 GCCGCTAAAGGCCATGTTCTTTAGCGGCGCT
35433625 GTATGACGGC
Statistics
Matches: 295, Mismatches: 37, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 295 1.00
ACGTcount: A:0.21, C:0.30, G:0.22, T:0.27
Consensus pattern (43 bp):
GCCGCTAAAGGCCATGTTCTTTAGCGGCGCTTTTCCCACAAAT
Found at i:35433400 original size:86 final size:86
Alignment explanation
Indices: 35433250--35433624 Score: 678
Period size: 86 Copynumber: 4.4 Consensus size: 86
35433240 AAAAATAAAC
* * * * * *
35433250 GCCGTTAAAGGTCATGTTCTTTAGCGGCGCTTTTCCCGCAAATGCCACTAAAGCCCATGTTCTTT
1 GCCGCTAAAGGCCATGTTCTTCAGCGGCGCTTTTCCCGCAAACGCCGCTAAAGGCCATGTTCTTT
* *
35433315 AGCGGCGCTTTTCCCACAAAT
66 AGTGGCGCTTTTCCCAAAAAT
35433336 GCCGCTAAAGGCCATGTTCTTCAGCGGCGCTTTTCCCGCAAACGCCGCTAAAGGCCATGTTCTTT
1 GCCGCTAAAGGCCATGTTCTTCAGCGGCGCTTTTCCCGCAAACGCCGCTAAAGGCCATGTTCTTT
35433401 AGTGGCGCTTTTCCCAAAAAT
66 AGTGGCGCTTTTCCCAAAAAT
35433422 GCCGCTAAAGGCCATGTTCTTCAGCGGCGCTTTTCCCGCAAACGCCGCTAAAGGCCATGTTCTTT
1 GCCGCTAAAGGCCATGTTCTTCAGCGGCGCTTTTCCCGCAAACGCCGCTAAAGGCCATGTTCTTT
35433487 AGTGGCGCTTTTCCCAAAAAT
66 AGTGGCGCTTTTCCCAAAAAT
35433508 GCCGCTAAAGGCCATGTTCTTCAGCGGCGCTTTTCCCGCAAACGCCGCTAAAGGCCATGTTCTTT
1 GCCGCTAAAGGCCATGTTCTTCAGCGGCGCTTTTCCCGCAAACGCCGCTAAAGGCCATGTTCTTT
35433573 AGTGGCGCTTTTCCCAAAAAT
66 AGTGGCGCTTTTCCCAAAAAT
35433594 GCCGCTAAAGGCCATGTTCTTCAGCGGCGCT
1 GCCGCTAAAGGCCATGTTCTTCAGCGGCGCT
35433625 GTATGACGGC
Statistics
Matches: 281, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
86 281 1.00
ACGTcount: A:0.21, C:0.30, G:0.22, T:0.27
Consensus pattern (86 bp):
GCCGCTAAAGGCCATGTTCTTCAGCGGCGCTTTTCCCGCAAACGCCGCTAAAGGCCATGTTCTTT
AGTGGCGCTTTTCCCAAAAAT
Found at i:35434066 original size:46 final size:46
Alignment explanation
Indices: 35434011--35434167 Score: 154
Period size: 46 Copynumber: 3.3 Consensus size: 46
35434001 CAATTGTGTG
* *
35434011 AGTTGTTAAGTTATTAAGTTATGTAAGTTATTATGTGAATTATATA
1 AGTTATTAAGTTATTAAGTTATGTAAGTTATTATGTAAATTATATA
* * * * *
35434057 AGTTATTAAGTTA-TATGGTATGACATATATATACGTATTATGTAAATTATGTG
1 AGTTATTAAGTTATTAAGTTATG---TA-A-GT---TATTATGTAAATTATATA
* *
35434110 AGTTGTTAAGTTGTTAAGTTATGTAAGTTATTATGTAAATTATATA
1 AGTTATTAAGTTATTAAGTTATGTAAGTTATTATGTAAATTATATA
35434156 AGTTATTAAGTT
1 AGTTATTAAGTT
35434168 GGACCAAATT
Statistics
Matches: 87, Mismatches: 15, Indels: 18
0.73 0.12 0.15
Matches are distributed among these distances:
45 7 0.08
46 39 0.45
48 2 0.02
49 2 0.02
50 2 0.02
51 2 0.02
53 26 0.30
54 7 0.08
ACGTcount: A:0.35, C:0.01, G:0.17, T:0.46
Consensus pattern (46 bp):
AGTTATTAAGTTATTAAGTTATGTAAGTTATTATGTAAATTATATA
Found at i:35434072 original size:17 final size:17
Alignment explanation
Indices: 35434017--35434072 Score: 58
Period size: 17 Copynumber: 3.1 Consensus size: 17
35434007 TGTGAGTTGT
*
35434017 TAAGTTATTAAGTTATG
1 TAAGTTATTAAGTTATA
*
35434034 TAAGTTATTATGTGAATTATA
1 TAAGTTATTA----AGTTATA
35434055 TAAGTTATTAAGTTATA
1 TAAGTTATTAAGTTATA
35434072 T
1 T
35434073 GGTATGACAT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
17 17 0.53
21 15 0.47
ACGTcount: A:0.38, C:0.00, G:0.14, T:0.48
Consensus pattern (17 bp):
TAAGTTATTAAGTTATA
Found at i:35434152 original size:21 final size:21
Alignment explanation
Indices: 35434092--35434163 Score: 72
Period size: 21 Copynumber: 3.2 Consensus size: 21
35434082 TATATATACG
*
35434092 TATTATGTAAATTATGTGAGT
1 TATTATGTAAATTATGTAAGT
* *
35434113 TGTTAAGTTGTTAAGTTATGTAAGT
1 TATT-A--TG-TAAATTATGTAAGT
*
35434138 TATTATGTAAATTATATAAGT
1 TATTATGTAAATTATGTAAGT
35434159 TATTA
1 TATTA
35434164 AGTTGGACCA
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
21 20 0.49
22 3 0.07
24 3 0.07
25 15 0.37
ACGTcount: A:0.35, C:0.00, G:0.17, T:0.49
Consensus pattern (21 bp):
TATTATGTAAATTATGTAAGT
Found at i:35434915 original size:57 final size:58
Alignment explanation
Indices: 35434832--35434949 Score: 229
Period size: 57 Copynumber: 2.1 Consensus size: 58
35434822 TAAATTGTAA
35434832 AATTTCAAATTTAAACGACCAAAAACAGAAACTGACCTAACTTTTAAAAATTTCTTAT
1 AATTTCAAATTTAAACGACCAAAAACAGAAACTGACCTAACTTTTAAAAATTTCTTAT
35434890 AATTTCAAATTT-AACGACCAAAAACAGAAACTGACCTAACTTTTAAAAATTTCTTAT
1 AATTTCAAATTTAAACGACCAAAAACAGAAACTGACCTAACTTTTAAAAATTTCTTAT
35434947 AAT
1 AAT
35434950 CCACCTTCTA
Statistics
Matches: 60, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
57 48 0.80
58 12 0.20
ACGTcount: A:0.47, C:0.17, G:0.05, T:0.31
Consensus pattern (58 bp):
AATTTCAAATTTAAACGACCAAAAACAGAAACTGACCTAACTTTTAAAAATTTCTTAT
Found at i:35436980 original size:199 final size:199
Alignment explanation
Indices: 35436640--35437241 Score: 864
Period size: 199 Copynumber: 3.0 Consensus size: 199
35436630 CATTGCGGCT
* * * *
35436640 TTTTTTAGTAGCGCCACTAATGCCCAGGCAAAACGACACCGTTTTGCGAAAACTGAGAAAAAAAA
1 TTTTTTAGTAGCACCACTAATGCCCAGGCAAAACGACACCGTTTTGCGAAAACTGAGAACAGAAC
* * * *
35436705 TTTATGGCGTTTTTTCCTTAGCGCCGCTAATGACCACATTTAGCTGCGTTTTTACCTTAGCGCCT
66 TTTACGGCGTTTTTTCCTTAGCGCCGCTAATGACCACATTTAGCGGCGTTTTTCCCTTAGCGCCA
* *
35436770 CAAAACCCATTAAATTCGCAGCCAAAAACTGCACCATTTTTTCTTCATTATTAAGAATATTTTAT
131 CAAAACCCATTAAATTCGCAGCCAAAAACTGCACCATTTTGTCTTCATTATTAAGAATATTTTGT
*
35436835 AGCG
196 GGCG
** * *
35436839 TTTTTTAGTAGTTCCACTAATGCCCAGGCAAAACGACATCGTTTTACGAAAACTGAGAACAGAAC
1 TTTTTTAGTAGCACCACTAATGCCCAGGCAAAACGACACCGTTTTGCGAAAACTGAGAACAGAAC
* *
35436904 TTTGCGGCGTTTTTTCCTTAGCGCCGCTAATGACCACATTTAGCGGCGTTTTTCCCTTAGCGCCG
66 TTTACGGCGTTTTTTCCTTAGCGCCGCTAATGACCACATTTAGCGGCGTTTTTCCCTTAGCGCCA
35436969 CAAAACCCATTAAATTCGCAGCCAAAAACTGCA-CAGTTTTGTCTTCATTATTAAGAATATTTTG
131 CAAAACCCATTAAATTCGCAGCCAAAAACTGCACCA-TTTTGTCTTCATTATTAAGAATATTTTG
* *
35437033 CGGTG
195 TGGCG
* * * * *
35437038 TTTTTTAGTAGCACCACTAATGCCCAGGAAAAATGACACCATTTTGCAAAAACTAAGAACAGAAC
1 TTTTTTAGTAGCACCACTAATGCCCAGGCAAAACGACACCGTTTTGCGAAAACTGAGAACAGAAC
* * * * * ** * *
35437103 CTTCCAGCGTTTTTTCCTTAGCACCGCTAATGACTACCCTTAGCGGCATTTTTCCCTTAACGCCA
66 TTTACGGCGTTTTTTCCTTAGCGCCGCTAATGACCACATTTAGCGGCGTTTTTCCCTTAGCGCCA
* * *
35437168 CAAAACCCATTAAATTCACAGCCCAAAACTGCACCGTTTTGTCTTCATTATTAAGAATATTTTGT
131 CAAAACCCATTAAATTCGCAGCCAAAAACTGCACCATTTTGTCTTCATTATTAAGAATATTTTGT
35437233 GGCG
196 GGCG
35437237 TTTTT
1 TTTTT
35437242 GTTCAAAACG
Statistics
Matches: 360, Mismatches: 41, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
198 2 0.01
199 357 0.99
200 1 0.00
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.31
Consensus pattern (199 bp):
TTTTTTAGTAGCACCACTAATGCCCAGGCAAAACGACACCGTTTTGCGAAAACTGAGAACAGAAC
TTTACGGCGTTTTTTCCTTAGCGCCGCTAATGACCACATTTAGCGGCGTTTTTCCCTTAGCGCCA
CAAAACCCATTAAATTCGCAGCCAAAAACTGCACCATTTTGTCTTCATTATTAAGAATATTTTGT
GGCG
Found at i:35437426 original size:48 final size:48
Alignment explanation
Indices: 35437350--35437457 Score: 144
Period size: 48 Copynumber: 2.2 Consensus size: 48
35437340 TTTTAATGCA
* * **
35437350 TAGTTTTGTTTAGGTAATATTTATAAAAATTAGATAAAATTATCAATTT
1 TAGTTTT-TTTAAGTAATATTTATAAAAATTAGATAAAAATAAAAATTT
* *
35437399 TAGTTTTTTTAAGTAGTATTTATAAAAATTAGGTAAAAATAAAAATTT
1 TAGTTTTTTTAAGTAATATTTATAAAAATTAGATAAAAATAAAAATTT
*
35437447 TAGTGTTTTTA
1 TAGTTTTTTTA
35437458 TTTCTTTTTA
Statistics
Matches: 52, Mismatches: 7, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
48 45 0.87
49 7 0.13
ACGTcount: A:0.41, C:0.01, G:0.11, T:0.47
Consensus pattern (48 bp):
TAGTTTTTTTAAGTAATATTTATAAAAATTAGATAAAAATAAAAATTT
Found at i:35437499 original size:10 final size:9
Alignment explanation
Indices: 35437477--35437523 Score: 69
Period size: 9 Copynumber: 5.2 Consensus size: 9
35437467 AATTTTTTAA
*
35437477 TTTATAATT
1 TTTACAATT
35437486 TTTACAATTT
1 TTTACAA-TT
35437496 TTTACAA-T
1 TTTACAATT
35437504 TTTACAATT
1 TTTACAATT
35437513 TTTACAATT
1 TTTACAATT
35437522 TT
1 TT
35437524 AAATTATTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
8 8 0.23
9 18 0.51
10 9 0.26
ACGTcount: A:0.32, C:0.09, G:0.00, T:0.60
Consensus pattern (9 bp):
TTTACAATT
Found at i:35437506 original size:8 final size:8
Alignment explanation
Indices: 35437485--35437528 Score: 54
Period size: 8 Copynumber: 5.2 Consensus size: 8
35437475 AATTTATAAT
35437485 TTTTACAA
1 TTTTACAA
35437493 TTTTTTACAA
1 --TTTTACAA
35437503 TTTTACAA
1 TTTTACAA
35437511 TTTTTACAA
1 -TTTTACAA
35437520 TTTTA-AA
1 TTTTACAA
35437527 TT
1 TT
35437529 ATTATATTCA
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
7 4 0.12
8 13 0.39
9 8 0.24
10 8 0.24
ACGTcount: A:0.34, C:0.09, G:0.00, T:0.57
Consensus pattern (8 bp):
TTTTACAA
Found at i:35437516 original size:17 final size:17
Alignment explanation
Indices: 35437485--35437528 Score: 72
Period size: 17 Copynumber: 2.6 Consensus size: 17
35437475 AATTTATAAT
35437485 TTTTACAATTTTTTACAA
1 TTTTACAA-TTTTTACAA
35437503 TTTTACAATTTTTACAA
1 TTTTACAATTTTTACAA
35437520 TTTTA-AATT
1 TTTTACAATT
35437529 ATTATATTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
16 4 0.15
17 14 0.54
18 8 0.31
ACGTcount: A:0.34, C:0.09, G:0.00, T:0.57
Consensus pattern (17 bp):
TTTTACAATTTTTACAA
Found at i:35437542 original size:21 final size:20
Alignment explanation
Indices: 35437517--35437571 Score: 51
Period size: 21 Copynumber: 2.6 Consensus size: 20
35437507 ACAATTTTTA
35437517 CAATTTTAAATTATT-ATATT
1 CAATTTTAAATTATTCATA-T
*
35437537 CAAATTATTATA-TATTGCATAT
1 C-AATT-TTAAATTATT-CATAT
35437559 CAATTTTAAATTA
1 CAATTTTAAATTA
35437572 ATAATCTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 9
0.72 0.05 0.23
Matches are distributed among these distances:
20 5 0.18
21 14 0.50
22 6 0.21
23 3 0.11
ACGTcount: A:0.42, C:0.07, G:0.02, T:0.49
Consensus pattern (20 bp):
CAATTTTAAATTATTCATAT
Found at i:35437869 original size:114 final size:114
Alignment explanation
Indices: 35437664--35438902 Score: 1940
Period size: 114 Copynumber: 10.9 Consensus size: 114
35437654 TAAATTATTT
* * *
35437664 TAAATCCCTGAGCATTAGCGGCGCTTACTTAAAAATGCCACTAAATCCCTGAAAGCTCAGAAAAC
1 TAAAGCCCTGAGCATTAGCGGCGCTTACTTAAAAACGCCACTAAATCCCCGAAAGCTCAGAAAAC
* * * *
35437729 GACGTCGTTGGGCTCAGGTATTTTTGCGGCACTTTCCCAAAAACGCTGC
66 GGCGTCGTTGGGCTTAGGTATTTTTGCGGCGCTTTCCCAAAAACGCCGC
* * *
35437778 GAAAGCCCTGAGCATTAGCAGCGCTTACTTAAAAACGCCACTAAATCCCCGAAAGCTCAGAAAAA
1 TAAAGCCCTGAGCATTAGCGGCGCTTACTTAAAAACGCCACTAAATCCCCGAAAGCTCAGAAAAC
35437843 GGCGTCGTTGGGCTTAGGTATTTTTGCGGCGCTTTCCCAAAAACGCCGC
66 GGCGTCGTTGGGCTTAGGTATTTTTGCGGCGCTTTCCCAAAAACGCCGC
* * *
35437892 TAAAGCCCGGAGCATTAGCGGCGCTTACTTAAAAATGCCACTAAATCCCTGAAAGCTCAGAAAAC
1 TAAAGCCCTGAGCATTAGCGGCGCTTACTTAAAAACGCCACTAAATCCCCGAAAGCTCAGAAAAC
* * * *
35437957 GACGTCGTTGGGCTCAGGTATTTTTGCGGCACTTTCCCAAAAACGCTGC
66 GGCGTCGTTGGGCTTAGGTATTTTTGCGGCGCTTTCCCAAAAACGCCGC
* * *
35438006 GAAAGCCCTGAGCATTAGCAGCGCTTACTTAAAAACGCCACTAAATCCCCGAAAGCTCAGAAAAA
1 TAAAGCCCTGAGCATTAGCGGCGCTTACTTAAAAACGCCACTAAATCCCCGAAAGCTCAGAAAAC
35438071 GGCGTCGTTGGGCTTAGGTATTTTTGCGGCGCTTTCCCAAAAACGCCGC
66 GGCGTCGTTGGGCTTAGGTATTTTTGCGGCGCTTTCCCAAAAACGCCGC
* * *
35438120 TAAAGCCCGGAGCATTAGCGGCGCTTACTTAAAAATGCCACTAAATCCCTGAAAGCTCAGAAAAC
1 TAAAGCCCTGAGCATTAGCGGCGCTTACTTAAAAACGCCACTAAATCCCCGAAAGCTCAGAAAAC
* * * *
35438185 GACGTCGTTGGGCTCAGGTATTTTTGCGGCACTTTCCCAAAAACGCTGC
66 GGCGTCGTTGGGCTTAGGTATTTTTGCGGCGCTTTCCCAAAAACGCCGC
* * *
35438234 GAAAGCCCTGAGCATTAGCAGCGCTTACTTAAAAACGCCACTAAATCCCCGAAAGCTCAGAAAAA
1 TAAAGCCCTGAGCATTAGCGGCGCTTACTTAAAAACGCCACTAAATCCCCGAAAGCTCAGAAAAC
35438299 GGCGTCGTTGGGCTTAGGTATTTTTGCGGCGCTTTCCCAAAAACGCCGC
66 GGCGTCGTTGGGCTTAGGTATTTTTGCGGCGCTTTCCCAAAAACGCCGC
* * *
35438348 TAAAGCCCGGAGCATTAGCGGCGCTTACTTAAAAATGCCACTAAATCCCTGAAAGCTCAGAAAAC
1 TAAAGCCCTGAGCATTAGCGGCGCTTACTTAAAAACGCCACTAAATCCCCGAAAGCTCAGAAAAC
* * * *
35438413 GACGTCGTTGGGCTCAGGTATTTTTGCGGCACTTTCCCAAAAACGCTGC
66 GGCGTCGTTGGGCTTAGGTATTTTTGCGGCGCTTTCCCAAAAACGCCGC
* * *
35438462 GAAAGCCCTGAGCATTAGCAGCGCTTACTTAAAAACGCCACTAAATCCCCGAAAGCTCAGAAAAA
1 TAAAGCCCTGAGCATTAGCGGCGCTTACTTAAAAACGCCACTAAATCCCCGAAAGCTCAGAAAAC
35438527 GGCGTCGTTGGGCTTAGGTATTTTTGCGGCGCTTTCCCAAAAACGCCGC
66 GGCGTCGTTGGGCTTAGGTATTTTTGCGGCGCTTTCCCAAAAACGCCGC
* * *
35438576 TAAAGCCCGGAGCATTAGCGGCGCTTACTTAAAAATGCCAGTAAATCCCCGAAAGCTCAGAAAAC
1 TAAAGCCCTGAGCATTAGCGGCGCTTACTTAAAAACGCCACTAAATCCCCGAAAGCTCAGAAAAC
* *
35438641 GGCGTCGTTGAGCTTAGGTATTTTTGCGGCGCTTTCCCAAAAATGCCGC
66 GGCGTCGTTGGGCTTAGGTATTTTTGCGGCGCTTTCCCAAAAACGCCGC
* * * *
35438690 TAAAGACCTGAGCATTAGCGGCGCTTACCTAAAAACCCCACTAAATCCCCAAAAGCTCAGAAAAC
1 TAAAGCCCTGAGCATTAGCGGCGCTTACTTAAAAACGCCACTAAATCCCCGAAAGCTCAGAAAAC
* * * * *
35438755 GACGTCGTTGGGCTTAGGTTTTTTTGTGGCGCTTTCTCAAAAACACCGC
66 GGCGTCGTTGGGCTTAGGTATTTTTGCGGCGCTTTCCCAAAAACGCCGC
* * * *
35438804 TAAAGCCTTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAAT
1 TAAAGCCCTGAGCATTAGCGGCGCTTACTTAAAAACGCCACTAAATCCCCGAAAGCTCAGAAAAC
*
35438869 GGCATCGTTGGGCTTAGGTA-TTTTGCGGCGCTTT
66 GGCGTCGTTGGGCTTAGGTATTTTTGCGGCGCTTT
35438903 TTGGAAAACG
Statistics
Matches: 1021, Mismatches: 104, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
113 13 0.01
114 1008 0.99
ACGTcount: A:0.29, C:0.26, G:0.22, T:0.23
Consensus pattern (114 bp):
TAAAGCCCTGAGCATTAGCGGCGCTTACTTAAAAACGCCACTAAATCCCCGAAAGCTCAGAAAAC
GGCGTCGTTGGGCTTAGGTATTTTTGCGGCGCTTTCCCAAAAACGCCGC
Found at i:35438070 original size:228 final size:228
Alignment explanation
Indices: 35437664--35438902 Score: 2174
Period size: 228 Copynumber: 5.4 Consensus size: 228
35437654 TAAATTATTT
* *
35437664 TAAATCCCTGAGCATTAGCGGCGCTTACTTAAAAATGCCACTAAATCCCTGAAAGCTCAGAAAAC
1 TAAAGCCCGGAGCATTAGCGGCGCTTACTTAAAAATGCCACTAAATCCCTGAAAGCTCAGAAAAC
35437729 GACGTCGTTGGGCTCAGGTATTTTTGCGGCACTTTCCCAAAAACGCTGCGAAAGCCCTGAGCATT
66 GACGTCGTTGGGCTCAGGTATTTTTGCGGCACTTTCCCAAAAACGCTGCGAAAGCCCTGAGCATT
35437794 AGCAGCGCTTACTTAAAAACGCCACTAAATCCCCGAAAGCTCAGAAAAAGGCGTCGTTGGGCTTA
131 AGCAGCGCTTACTTAAAAACGCCACTAAATCCCCGAAAGCTCAGAAAAAGGCGTCGTTGGGCTTA
35437859 GGTATTTTTGCGGCGCTTTCCCAAAAACGCCGC
196 GGTATTTTTGCGGCGCTTTCCCAAAAACGCCGC
35437892 TAAAGCCCGGAGCATTAGCGGCGCTTACTTAAAAATGCCACTAAATCCCTGAAAGCTCAGAAAAC
1 TAAAGCCCGGAGCATTAGCGGCGCTTACTTAAAAATGCCACTAAATCCCTGAAAGCTCAGAAAAC
35437957 GACGTCGTTGGGCTCAGGTATTTTTGCGGCACTTTCCCAAAAACGCTGCGAAAGCCCTGAGCATT
66 GACGTCGTTGGGCTCAGGTATTTTTGCGGCACTTTCCCAAAAACGCTGCGAAAGCCCTGAGCATT
35438022 AGCAGCGCTTACTTAAAAACGCCACTAAATCCCCGAAAGCTCAGAAAAAGGCGTCGTTGGGCTTA
131 AGCAGCGCTTACTTAAAAACGCCACTAAATCCCCGAAAGCTCAGAAAAAGGCGTCGTTGGGCTTA
35438087 GGTATTTTTGCGGCGCTTTCCCAAAAACGCCGC
196 GGTATTTTTGCGGCGCTTTCCCAAAAACGCCGC
35438120 TAAAGCCCGGAGCATTAGCGGCGCTTACTTAAAAATGCCACTAAATCCCTGAAAGCTCAGAAAAC
1 TAAAGCCCGGAGCATTAGCGGCGCTTACTTAAAAATGCCACTAAATCCCTGAAAGCTCAGAAAAC
35438185 GACGTCGTTGGGCTCAGGTATTTTTGCGGCACTTTCCCAAAAACGCTGCGAAAGCCCTGAGCATT
66 GACGTCGTTGGGCTCAGGTATTTTTGCGGCACTTTCCCAAAAACGCTGCGAAAGCCCTGAGCATT
35438250 AGCAGCGCTTACTTAAAAACGCCACTAAATCCCCGAAAGCTCAGAAAAAGGCGTCGTTGGGCTTA
131 AGCAGCGCTTACTTAAAAACGCCACTAAATCCCCGAAAGCTCAGAAAAAGGCGTCGTTGGGCTTA
35438315 GGTATTTTTGCGGCGCTTTCCCAAAAACGCCGC
196 GGTATTTTTGCGGCGCTTTCCCAAAAACGCCGC
35438348 TAAAGCCCGGAGCATTAGCGGCGCTTACTTAAAAATGCCACTAAATCCCTGAAAGCTCAGAAAAC
1 TAAAGCCCGGAGCATTAGCGGCGCTTACTTAAAAATGCCACTAAATCCCTGAAAGCTCAGAAAAC
35438413 GACGTCGTTGGGCTCAGGTATTTTTGCGGCACTTTCCCAAAAACGCTGCGAAAGCCCTGAGCATT
66 GACGTCGTTGGGCTCAGGTATTTTTGCGGCACTTTCCCAAAAACGCTGCGAAAGCCCTGAGCATT
35438478 AGCAGCGCTTACTTAAAAACGCCACTAAATCCCCGAAAGCTCAGAAAAAGGCGTCGTTGGGCTTA
131 AGCAGCGCTTACTTAAAAACGCCACTAAATCCCCGAAAGCTCAGAAAAAGGCGTCGTTGGGCTTA
35438543 GGTATTTTTGCGGCGCTTTCCCAAAAACGCCGC
196 GGTATTTTTGCGGCGCTTTCCCAAAAACGCCGC
* *
35438576 TAAAGCCCGGAGCATTAGCGGCGCTTACTTAAAAATGCCAGTAAATCCCCGAAAGCTCAGAAAAC
1 TAAAGCCCGGAGCATTAGCGGCGCTTACTTAAAAATGCCACTAAATCCCTGAAAGCTCAGAAAAC
* * * * * * * *
35438641 GGCGTCGTTGAGCTTAGGTATTTTTGCGGCGCTTTCCCAAAAATGCCGCTAAAGACCTGAGCATT
66 GACGTCGTTGGGCTCAGGTATTTTTGCGGCACTTTCCCAAAAACGCTGCGAAAGCCCTGAGCATT
* * * * * *
35438706 AGCGGCGCTTACCTAAAAACCCCACTAAATCCCCAAAAGCTCAGAAAACGACGTCGTTGGGCTTA
131 AGCAGCGCTTACTTAAAAACGCCACTAAATCCCCGAAAGCTCAGAAAAAGGCGTCGTTGGGCTTA
* * * *
35438771 GGTTTTTTTGTGGCGCTTTCTCAAAAACACCGC
196 GGTATTTTTGCGGCGCTTTCCCAAAAACGCCGC
** * * * * *
35438804 TAAAGCCTTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAAT
1 TAAAGCCCGGAGCATTAGCGGCGCTTACTTAAAAATGCCACTAAATCCCTGAAAGCTCAGAAAAC
* * * *
35438869 GGCATCGTTGGGCTTAGGTA-TTTTGCGGCGCTTT
66 GACGTCGTTGGGCTCAGGTATTTTTGCGGCACTTT
35438903 TTGGAAAACG
Statistics
Matches: 980, Mismatches: 31, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
227 14 0.01
228 966 0.99
ACGTcount: A:0.29, C:0.26, G:0.22, T:0.23
Consensus pattern (228 bp):
TAAAGCCCGGAGCATTAGCGGCGCTTACTTAAAAATGCCACTAAATCCCTGAAAGCTCAGAAAAC
GACGTCGTTGGGCTCAGGTATTTTTGCGGCACTTTCCCAAAAACGCTGCGAAAGCCCTGAGCATT
AGCAGCGCTTACTTAAAAACGCCACTAAATCCCCGAAAGCTCAGAAAAAGGCGTCGTTGGGCTTA
GGTATTTTTGCGGCGCTTTCCCAAAAACGCCGC
Found at i:35439820 original size:23 final size:21
Alignment explanation
Indices: 35439761--35439820 Score: 59
Period size: 22 Copynumber: 2.8 Consensus size: 21
35439751 CTCAAATCTA
*
35439761 TTAAT-TTGATTTAAATTTAT
1 TTAATATTGATTTAAAATTAT
* *
35439781 TTAGTAGTGCATTTAAAATTAT
1 TTAATATTG-ATTTAAAATTAT
35439803 TATAATATTGATTCTAAA
1 T-TAATATTGATT-TAAA
35439821 TTGTAGTTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
20 4 0.13
21 2 0.06
22 15 0.48
23 10 0.32
ACGTcount: A:0.38, C:0.03, G:0.08, T:0.50
Consensus pattern (21 bp):
TTAATATTGATTTAAAATTAT
Found at i:35440252 original size:24 final size:24
Alignment explanation
Indices: 35440216--35440265 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
35440206 AATAGAAAAT
* *
35440216 AAAGAAGAAAAAA-AAAGAAAGTTA
1 AAAGAACAAAAAAGAAA-AAAATTA
*
35440240 AAAGAACATAAAAGAAAAAAATTA
1 AAAGAACAAAAAAGAAAAAAATTA
35440264 AA
1 AA
35440266 TTGCTCAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 19 0.86
25 3 0.14
ACGTcount: A:0.76, C:0.02, G:0.12, T:0.10
Consensus pattern (24 bp):
AAAGAACAAAAAAGAAAAAAATTA
Found at i:35443647 original size:43 final size:43
Alignment explanation
Indices: 35443586--35443671 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 43
35443576 CATGAAGGAG
*
35443586 TTACAATCCTATGAGTTGATGTTGAACGACGGTCAACCGATCC
1 TTACAATCCTATGAGTTGATGATGAACGACGGTCAACCGATCC
35443629 TTACAATCCTATGAGTTGATGATGAACGACGGTCAACCGATCC
1 TTACAATCCTATGAGTTGATGATGAACGACGGTCAACCGATCC
35443672 AAAAAGTATA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.27
Consensus pattern (43 bp):
TTACAATCCTATGAGTTGATGATGAACGACGGTCAACCGATCC
Found at i:35443711 original size:23 final size:23
Alignment explanation
Indices: 35443678--35443726 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
35443668 ATCCAAAAAG
35443678 TATATGAGAATATAGTCGTCACT
1 TATATGAGAATATAGTCGTCACT
*
35443701 TATATGCGAATATAGTCGTCACT
1 TATATGAGAATATAGTCGTCACT
35443724 TAT
1 TAT
35443727 GTAACACCCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (23 bp):
TATATGAGAATATAGTCGTCACT
Found at i:35445382 original size:42 final size:42
Alignment explanation
Indices: 35445336--35445574 Score: 250
Period size: 42 Copynumber: 5.7 Consensus size: 42
35445326 TCTAAAGCTG
* * * *
35445336 AACAGAAGCTCGTAAAAGCTAAACAGAAAC-CTATAAGGGTTG
1 AACAGAAGCTCATAAAAGCTGAACAGAAACTC-ATAAGAGTTA
* * *
35445378 AACAGAAGCTCATAAGAGCTGAACAAAAACTCATAAGGGTTA
1 AACAGAAGCTCATAAAAGCTGAACAGAAACTCATAAGAGTTA
* *
35445420 AACAGAAGCTCA-AAAGAGCTGAACGGAAACTCATATGAGTTA
1 AACAGAAGCTCATAAA-AGCTGAACAGAAACTCATAAGAGTTA
* * * *
35445462 AATAGAAGCTCATAAGAGCTGAACAGAAACTTATAAGAGTTG
1 AACAGAAGCTCATAAAAGCTGAACAGAAACTCATAAGAGTTA
** * * *
35445504 AGTAGAAGCTCGA-AAGAGCTGAACGGAAACTCATATGAGTTA
1 AACAGAAGCTC-ATAAAAGCTGAACAGAAACTCATAAGAGTTA
* *
35445546 AACAGAAGCTCATAAGAGCTAAACAGAAA
1 AACAGAAGCTCATAAAAGCTGAACAGAAA
35445575 GTAAAACATG
Statistics
Matches: 167, Mismatches: 25, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
41 3 0.02
42 160 0.96
43 4 0.02
ACGTcount: A:0.46, C:0.15, G:0.21, T:0.17
Consensus pattern (42 bp):
AACAGAAGCTCATAAAAGCTGAACAGAAACTCATAAGAGTTA
Found at i:35445497 original size:21 final size:21
Alignment explanation
Indices: 35445317--35445574 Score: 191
Period size: 21 Copynumber: 12.4 Consensus size: 21
35445307 GTACATCATT
*
35445317 AACAGAAGCTC-TAA-AGCTG
1 AACAGAAACTCATAAGAGCTG
* * * *
35445336 AACAGAAGCTCGTAAAAGCTA
1 AACAGAAACTCATAAGAGCTG
* *
35445357 AACAGAAAC-CTATAAGGGTTG
1 AACAGAAACTC-ATAAGAGCTG
*
35445378 AACAGAAGCTCATAAGAGCTG
1 AACAGAAACTCATAAGAGCTG
* * * *
35445399 AACAAAAACTCATAAGGGTTA
1 AACAGAAACTCATAAGAGCTG
* *
35445420 AACAGAAGCTCAAAAGAGCTG
1 AACAGAAACTCATAAGAGCTG
* * * *
35445441 AACGGAAACTCATATGAGTTA
1 AACAGAAACTCATAAGAGCTG
* *
35445462 AATAGAAGCTCATAAGAGCTG
1 AACAGAAACTCATAAGAGCTG
* *
35445483 AACAGAAACTTATAAGAGTTG
1 AACAGAAACTCATAAGAGCTG
** *
35445504 AGTAGAAGCTCGA-AAGAGCTG
1 AACAGAAACTC-ATAAGAGCTG
* * * *
35445525 AACGGAAACTCATATGAGTTA
1 AACAGAAACTCATAAGAGCTG
* *
35445546 AACAGAAGCTCATAAGAGCTA
1 AACAGAAACTCATAAGAGCTG
35445567 AACAGAAA
1 AACAGAAA
35445575 GTAAAACATG
Statistics
Matches: 179, Mismatches: 54, Indels: 10
0.74 0.22 0.04
Matches are distributed among these distances:
19 11 0.06
20 5 0.03
21 161 0.90
22 2 0.01
ACGTcount: A:0.46, C:0.16, G:0.21, T:0.17
Consensus pattern (21 bp):
AACAGAAACTCATAAGAGCTG
Found at i:35445571 original size:84 final size:84
Alignment explanation
Indices: 35445336--35445574 Score: 320
Period size: 84 Copynumber: 2.8 Consensus size: 84
35445326 TCTAAAGCTG
* * * * *
35445336 AACAGAAGCTCGTAAA-AGCTAAACAGAAAC-CTATAAGGGTTGAACAGAAGCTCATAAGAGCTG
1 AACAGAAGCTCG-AAAGAGCTGAACGGAAACTC-ATATGAGTTAAACAGAAGCTCATAAGAGCTG
* *
35445399 AACAAAAACTCATAAGGGTTA
64 AACAGAAACTCATAAGAGTTA
* *
35445420 AACAGAAGCTCAAAAGAGCTGAACGGAAACTCATATGAGTTAAATAGAAGCTCATAAGAGCTGAA
1 AACAGAAGCTCGAAAGAGCTGAACGGAAACTCATATGAGTTAAACAGAAGCTCATAAGAGCTGAA
* *
35445485 CAGAAACTTATAAGAGTTG
66 CAGAAACTCATAAGAGTTA
** *
35445504 AGTAGAAGCTCGAAAGAGCTGAACGGAAACTCATATGAGTTAAACAGAAGCTCATAAGAGCTAAA
1 AACAGAAGCTCGAAAGAGCTGAACGGAAACTCATATGAGTTAAACAGAAGCTCATAAGAGCTGAA
35445569 CAGAAA
66 CAGAAA
35445575 GTAAAACATG
Statistics
Matches: 137, Mismatches: 16, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
83 3 0.02
84 133 0.97
85 1 0.01
ACGTcount: A:0.46, C:0.15, G:0.21, T:0.17
Consensus pattern (84 bp):
AACAGAAGCTCGAAAGAGCTGAACGGAAACTCATATGAGTTAAACAGAAGCTCATAAGAGCTGAA
CAGAAACTCATAAGAGTTA
Found at i:35447849 original size:71 final size:71
Alignment explanation
Indices: 35447708--35447875 Score: 198
Period size: 71 Copynumber: 2.4 Consensus size: 71
35447698 AACCAAAGTG
* * * *
35447708 CTACTGATACCCTGAAGACTTCTACCAAGACAAGTCAAGTCAATAGCCAAAGTTCAACATCTCCT
1 CTACCGATACCTTGAGGACTTCTACCAAAACAAGTCAAGTCAATAGCCAAAGTTCAACATCTCCT
*
35447773 GCACTT
66 ACACTT
* * *
35447779 CTACCGATACCTTGAGGACTTCTACCAAAACAAGTCAAGTCAGTAGCCAAAGTTTAGCATC-CTC
1 CTACCGATACCTTGAGGACTTCTACCAAAACAAGTCAAGTCAATAGCCAAAGTTCAACATCTC-C
35447843 TACACTT
65 TACACTT
* *
35447850 TTATCGAT-CCTTTGATGGA-TTCTACC
1 CTACCGATACC-TTGA-GGACTTCTACC
35447876 GATACCAAAT
Statistics
Matches: 84, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
70 3 0.04
71 78 0.93
72 3 0.04
ACGTcount: A:0.31, C:0.28, G:0.14, T:0.27
Consensus pattern (71 bp):
CTACCGATACCTTGAGGACTTCTACCAAAACAAGTCAAGTCAATAGCCAAAGTTCAACATCTCCT
ACACTT
Found at i:35452738 original size:7 final size:6
Alignment explanation
Indices: 35452716--35452802 Score: 66
Period size: 6 Copynumber: 13.8 Consensus size: 6
35452706 GAAGTTTAAG
* * * *
35452716 AAAATA AAAATAA AAAACTA AAAACA AAAACA AAAATA AAAAGA AACATA
1 AAAATA AAAAT-A AAAA-TA AAAATA AAAATA AAAATA AAAATA AAAATA
* * * *
35452766 AAAAGA AAAAGA AAACTA AAAAGA AAACATA TAAAAT
1 AAAATA AAAATA AAAATA AAAATA AAA-ATA -AAAAT
35452803 CAATGGTCCT
Statistics
Matches: 65, Mismatches: 12, Indels: 7
0.77 0.14 0.08
Matches are distributed among these distances:
6 47 0.72
7 14 0.22
8 4 0.06
ACGTcount: A:0.78, C:0.07, G:0.05, T:0.10
Consensus pattern (6 bp):
AAAATA
Found at i:35452755 original size:18 final size:18
Alignment explanation
Indices: 35452716--35452792 Score: 73
Period size: 18 Copynumber: 4.2 Consensus size: 18
35452706 GAAGTTTAAG
* *
35452716 AAAATAAAAATAAAAAACTA
1 AAAAGAAAAAT-AAAAA-GA
* * *
35452736 AAAACAAAAACAAAAATA
1 AAAAGAAAAATAAAAAGA
*
35452754 AAAAGAAACATAAAAAGA
1 AAAAGAAAAATAAAAAGA
*
35452772 AAAAGAAAACTAAAAAGA
1 AAAAGAAAAATAAAAAGA
35452790 AAA
1 AAA
35452793 CATATAAAAT
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
18 35 0.71
19 5 0.10
20 9 0.18
ACGTcount: A:0.81, C:0.06, G:0.05, T:0.08
Consensus pattern (18 bp):
AAAAGAAAAATAAAAAGA
Found at i:35454481 original size:28 final size:29
Alignment explanation
Indices: 35454450--35454518 Score: 83
Period size: 28 Copynumber: 2.5 Consensus size: 29
35454440 AAAAAAAAGC
35454450 AGAATAATAAAATAA-AATAAAATAATAA
1 AGAATAATAAAATAATAATAAAATAATAA
*
35454478 AGAA-ATTAAAGA-AATAATAAAATAATAA
1 AGAATAATAAA-ATAATAATAAAATAATAA
*
35454506 AGAATTA-AAAATA
1 AGAATAATAAAATA
35454519 GGGGAAATAA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
27 8 0.24
28 26 0.76
ACGTcount: A:0.72, C:0.00, G:0.06, T:0.22
Consensus pattern (29 bp):
AGAATAATAAAATAATAATAAAATAATAA
Found at i:35461544 original size:24 final size:25
Alignment explanation
Indices: 35461495--35461544 Score: 59
Period size: 24 Copynumber: 2.0 Consensus size: 25
35461485 AAAAATGGAT
* *
35461495 AATTAATTGTTGTCCTTAAAATAGG
1 AATTAATTGTTGTCCATAAAAAAGG
35461520 AATT-ATTGTT-TCCATAAGAAAAGG
1 AATTAATTGTTGTCCATAA-AAAAGG
35461544 A
1 A
35461545 CATAAGTCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
23 6 0.27
24 12 0.55
25 4 0.18
ACGTcount: A:0.40, C:0.08, G:0.16, T:0.36
Consensus pattern (25 bp):
AATTAATTGTTGTCCATAAAAAAGG
Found at i:35466603 original size:21 final size:21
Alignment explanation
Indices: 35466577--35466619 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
35466567 GTAGTACTTT
*
35466577 TGAGTTAGTAAAAAAAATTCA
1 TGAGTTAGTAAAAAAAAATCA
35466598 TGAGTTAGTAAAAAAAAATCA
1 TGAGTTAGTAAAAAAAAATCA
35466619 T
1 T
35466620 TTATTAAGTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.53, C:0.05, G:0.14, T:0.28
Consensus pattern (21 bp):
TGAGTTAGTAAAAAAAAATCA
Found at i:35473629 original size:37 final size:37
Alignment explanation
Indices: 35473577--35473663 Score: 149
Period size: 37 Copynumber: 2.4 Consensus size: 37
35473567 ACACAAGCAG
*
35473577 TCCAACCGA-AACATGCCAAATGCTCATGAGAGCTAA
1 TCCAACCGATAACATGCCAAATGCTCATAAGAGCTAA
*
35473613 TCTAACCGATAACATGCCAAATGCTCATAAGAGCTAA
1 TCCAACCGATAACATGCCAAATGCTCATAAGAGCTAA
35473650 TCCAACCGATAACA
1 TCCAACCGATAACA
35473664 CCCCTCGACA
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
36 8 0.17
37 39 0.83
ACGTcount: A:0.40, C:0.28, G:0.14, T:0.18
Consensus pattern (37 bp):
TCCAACCGATAACATGCCAAATGCTCATAAGAGCTAA
Found at i:35479339 original size:15 final size:15
Alignment explanation
Indices: 35479319--35479359 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
35479309 CGATGTATAA
*
35479319 TGTGATATGTGATTG
1 TGTGATATGTGATCG
*
35479334 TGTGATACGTGATCG
1 TGTGATATGTGATCG
*
35479349 TGTGGTATGTG
1 TGTGATATGTG
35479360 TAAAACATGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.17, C:0.05, G:0.37, T:0.41
Consensus pattern (15 bp):
TGTGATATGTGATCG
Found at i:35482316 original size:25 final size:26
Alignment explanation
Indices: 35482282--35482372 Score: 106
Period size: 25 Copynumber: 3.8 Consensus size: 26
35482272 ATTCTATTTG
*
35482282 GCCTTTGTGGTGTATCT-TGTATGTT
1 GCCTTTGTGGCGTATCTCTGTATGTT
*
35482307 GCCTTTGTGGCGTA-CTCTG-A--TA
1 GCCTTTGTGGCGTATCTCTGTATGTT
*
35482329 GACTTTGTGGCGTAT-TCTGTATGTT
1 GCCTTTGTGGCGTATCTCTGTATGTT
35482354 GCCTTTGTGGCGT-TCTCTG
1 GCCTTTGTGGCGTATCTCTG
35482373 ATAATATTTG
Statistics
Matches: 55, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
22 18 0.33
23 1 0.02
24 4 0.07
25 32 0.58
ACGTcount: A:0.09, C:0.18, G:0.29, T:0.45
Consensus pattern (26 bp):
GCCTTTGTGGCGTATCTCTGTATGTT
Found at i:35482337 original size:22 final size:22
Alignment explanation
Indices: 35482309--35482375 Score: 71
Period size: 22 Copynumber: 2.9 Consensus size: 22
35482299 TGTATGTTGC
35482309 CTTTGTGGCGTACTCTGATAGA
1 CTTTGTGGCGTACTCTGATAGA
* * *
35482331 CTTTGTGGCGTATTCTGTATGTTGC
1 CTTTGTGGCGTACTCTG-A--TAGA
*
35482356 CTTTGTGGCGTTCTCTGATA
1 CTTTGTGGCGTACTCTGATA
35482376 ATATTTGGGG
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
22 17 0.47
23 1 0.03
24 1 0.03
25 17 0.47
ACGTcount: A:0.12, C:0.18, G:0.27, T:0.43
Consensus pattern (22 bp):
CTTTGTGGCGTACTCTGATAGA
Found at i:35482353 original size:47 final size:47
Alignment explanation
Indices: 35482284--35482467 Score: 180
Period size: 47 Copynumber: 4.0 Consensus size: 47
35482274 TCTATTTGGC
*
35482284 CTTTGTGGTGTA-TCTTGTATGTTGCCTTTGTGGCGTACTCTGATAGA
1 CTTTGTGGCGTATTC-TGTATGTTGCCTTTGTGGCGTACTCTGATAGA
*
35482331 CTTTGTGGCGTATTCTGTATGTTGCCTTTGTGGCGTTCTCTGATA-A
1 CTTTGTGGCGTATTCTGTATGTTGCCTTTGTGGCGTACTCTGATAGA
* * * ** * *
35482377 TATTTGGGGTGTATTCTGTATGTTTTCTTTGTGGTGTACTCTGGTAG-
1 -CTTTGTGGCGTATTCTGTATGTTGCCTTTGTGGCGTACTCTGATAGA
* * * * *
35482424 CTTTTGTGGCTTATTCCGTCTG--GCCCTTGTGGCATACTCTGATA
1 C-TTTGTGGCGTATTCTGTATGTTGCCTTTGTGGCGTACTCTGATA
35482468 AGTTTATGTT
Statistics
Matches: 111, Mismatches: 22, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
45 16 0.14
46 1 0.01
47 92 0.83
48 2 0.02
ACGTcount: A:0.11, C:0.16, G:0.27, T:0.46
Consensus pattern (47 bp):
CTTTGTGGCGTATTCTGTATGTTGCCTTTGTGGCGTACTCTGATAGA
Found at i:35484023 original size:23 final size:22
Alignment explanation
Indices: 35483958--35484023 Score: 62
Period size: 23 Copynumber: 2.9 Consensus size: 22
35483948 TTGGTGGGAG
* *
35483958 CATTCTGGCACTATAATGCAATT
1 CATTTTGGCACT-TAATGCAACT
*
35483981 CATTTTGGCA-TTGATGTGCAACT
1 CATTTTGGCACTT-A-ATGCAACT
35484004 CATTTTGGCACTTCAATGCA
1 CATTTTGGCACTT-AATGCA
35484024 TTACATTTTG
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
21 1 0.03
22 2 0.06
23 29 0.83
24 3 0.09
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (22 bp):
CATTTTGGCACTTAATGCAACT
Found at i:35485354 original size:19 final size:17
Alignment explanation
Indices: 35485330--35485364 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
35485320 ATTATTTGAA
35485330 TATTATATAATTCTTGTTT
1 TATTAT-TAATT-TTGTTT
35485349 TATTATTAATTTTGTT
1 TATTATTAATTTTGTT
35485365 ACTATTTTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 5 0.31
19 6 0.38
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.66
Consensus pattern (17 bp):
TATTATTAATTTTGTTT
Found at i:35485370 original size:18 final size:19
Alignment explanation
Indices: 35485330--35485370 Score: 50
Period size: 18 Copynumber: 2.2 Consensus size: 19
35485320 ATTATTTGAA
*
35485330 TATTATATAATTCTTGTTT
1 TATTATATAATTCTTGTTC
35485349 TATTAT-TAATT-TTGTTAC
1 TATTATATAATTCTTGTT-C
35485367 TATT
1 TATT
35485371 TTAGAAGTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 5 0.25
18 9 0.45
19 6 0.30
ACGTcount: A:0.27, C:0.05, G:0.05, T:0.63
Consensus pattern (19 bp):
TATTATATAATTCTTGTTC
Found at i:35496732 original size:25 final size:25
Alignment explanation
Indices: 35496704--35496820 Score: 78
Period size: 25 Copynumber: 4.6 Consensus size: 25
35496694 TTACCTTACA
*
35496704 GGCTTTCCAGATAACTCGCCACAAG
1 GGCTTTCCAGATAACTCACCACAAG
* *
35496729 GGCTTCCCA-A-ACATTACACCACATAG
1 GGCTTTCCAGATA-ACT-CACCACA-AG
* * *
35496755 GCCTTT-CAGAAAATTCACCACAAG
1 GGCTTTCCAGATAACTCACCACAAG
* * *
35496779 GGCTTCCCAGATAACCTCGCCACAAA
1 GGCTTTCCAGATAA-CTCACCACAAG
*
35496805 GGCTTTACTAGATAAC
1 GGCTTT-CCAGATAAC
35496821 CTGCCATAAA
Statistics
Matches: 71, Mismatches: 13, Indels: 15
0.72 0.13 0.15
Matches are distributed among these distances:
23 1 0.01
24 9 0.13
25 29 0.41
26 24 0.34
27 8 0.11
ACGTcount: A:0.32, C:0.32, G:0.15, T:0.21
Consensus pattern (25 bp):
GGCTTTCCAGATAACTCACCACAAG
Found at i:35496801 original size:26 final size:26
Alignment explanation
Indices: 35496772--35496838 Score: 73
Period size: 26 Copynumber: 2.6 Consensus size: 26
35496762 AGAAAATTCA
* *
35496772 CCACAAGGGC-TTCCCAGATAACCTCG
1 CCACAAAGGCTTTACCAGATAACCT-G
*
35496798 CCACAAAGGCTTTACTAGATAACCTG
1 CCACAAAGGCTTTACCAGATAACCTG
* *
35496824 CCATAAATGCTTTAC
1 CCACAAAGGCTTTAC
35496839 ACAAACTGTT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
26 23 0.66
27 12 0.34
ACGTcount: A:0.31, C:0.31, G:0.15, T:0.22
Consensus pattern (26 bp):
CCACAAAGGCTTTACCAGATAACCTG
Found at i:35496817 original size:27 final size:26
Alignment explanation
Indices: 35496787--35496838 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
35496777 AGGGCTTCCC
35496787 AGATAACCTCGCCACAAAGGCTTTACT
1 AGATAACCT-GCCACAAAGGCTTTACT
* *
35496814 AGATAACCTGCCATAAATGCTTTAC
1 AGATAACCTGCCACAAAGGCTTTAC
35496839 ACAAACTGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 14 0.61
27 9 0.39
ACGTcount: A:0.35, C:0.27, G:0.13, T:0.25
Consensus pattern (26 bp):
AGATAACCTGCCACAAAGGCTTTACT
Found at i:35497654 original size:40 final size:40
Alignment explanation
Indices: 35497599--35497679 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
35497589 CACACATTGG
35497599 ATACACAAATCTCTATCACATCAATGACTCAAAGAGTCTA
1 ATACACAAATCTCTATCACATCAATGACTCAAAGAGTCTA
35497639 ATACACAAATCTCTATCACATCAATGACTCAAAGAGTCTA
1 ATACACAAATCTCTATCACATCAATGACTCAAAGAGTCTA
35497679 A
1 A
35497680 CATATCTCAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.43, C:0.25, G:0.07, T:0.25
Consensus pattern (40 bp):
ATACACAAATCTCTATCACATCAATGACTCAAAGAGTCTA
Found at i:35501433 original size:27 final size:27
Alignment explanation
Indices: 35501405--35501777 Score: 315
Period size: 27 Copynumber: 13.9 Consensus size: 27
35501395 TCATCTTCTA
** *
35501405 GGGGTATAACAGTCATTTTACCCTATA
1 GGGGTATTTCAGTCATTTTACCCTATG
** * * *
35501432 GGGGTATTTTGGTCATTCTACCGTCTG
1 GGGGTATTTCAGTCATTTTACCCTATG
* *
35501459 GGGGTATTTCGGTCATTCTACCCTATG
1 GGGGTATTTCAGTCATTTTACCCTATG
*
35501486 GGGGTATTTTAGTCATTTTACCCTATG
1 GGGGTATTTCAGTCATTTTACCCTATG
* *
35501513 GGGCTATTTCAGTTATTTTACCCTATG
1 GGGGTATTTCAGTCATTTTACCCTATG
* * *
35501540 GGGGTATTTC-GATTATTTTATCTTATG
1 GGGGTATTTCAG-TCATTTTACCCTATG
* *
35501567 GGGGTATTTCAATTATTTTACCCTATG
1 GGGGTATTTCAGTCATTTTACCCTATG
** *
35501594 ATGGTATTTCGGTCATTTTACCCTAT-
1 GGGGTATTTCAGTCATTTTACCCTATG
* * *
35501620 GGGGTATTTCGGTTATTCTACCCTATG
1 GGGGTATTTCAGTCATTTTACCCTATG
*** *
35501647 GGGGTATTTTTTTCATTCTACCCTATG
1 GGGGTATTTCAGTCATTTTACCCTATG
* * * *
35501674 GAGGTATTT-TGATTATTTTATCCC-ATA
1 GGGGTATTTCAG-TCATTTTA-CCCTATG
* *
35501701 GGGGTATTTCGGTCATTTTACCTTATG
1 GGGGTATTTCAGTCATTTTACCCTATG
* * *
35501728 AGGGTACTTT-GGTCATTTTACACTATG
1 GGGGTA-TTTCAGTCATTTTACCCTATG
* **
35501755 AGGGTATTTTGGTCATTTTACCC
1 GGGGTATTTCAGTCATTTTACCC
35501778 ATTTTGGGGT
Statistics
Matches: 287, Mismatches: 50, Indels: 18
0.81 0.14 0.05
Matches are distributed among these distances:
26 29 0.10
27 251 0.87
28 7 0.02
ACGTcount: A:0.19, C:0.16, G:0.21, T:0.43
Consensus pattern (27 bp):
GGGGTATTTCAGTCATTTTACCCTATG
Found at i:35501463 original size:54 final size:54
Alignment explanation
Indices: 35501405--35501777 Score: 367
Period size: 54 Copynumber: 6.9 Consensus size: 54
35501395 TCATCTTCTA
** * * * * *
35501405 GGGGTATAACAGTCATTTTACCCTATAGGGGTATTTTGGTCATTCTACCGTCTG
1 GGGGTATTTCAGTTATTTTACCCTATGGGGGTATTTTGGTCATTTTACCCTATG
* * * *
35501459 GGGGTATTTCGGTCATTCTACCCTATGGGGGTATTTTAGTCATTTTACCCTATG
1 GGGGTATTTCAGTTATTTTACCCTATGGGGGTATTTTGGTCATTTTACCCTATG
* * * * * *
35501513 GGGCTATTTCAGTTATTTTACCCTATGGGGGTATTTCGATTATTTTATCTTATG
1 GGGGTATTTCAGTTATTTTACCCTATGGGGGTATTTTGGTCATTTTACCCTATG
* ** *
35501567 GGGGTATTTCAATTATTTTACCCTATGATGGTATTTCGGTCATTTTACCCTAT-
1 GGGGTATTTCAGTTATTTTACCCTATGGGGGTATTTTGGTCATTTTACCCTATG
* * ** *
35501620 GGGGTATTTCGGTTATTCTACCCTATGGGGGTATTTTTTTCATTCTACCCTATG
1 GGGGTATTTCAGTTATTTTACCCTATGGGGGTATTTTGGTCATTTTACCCTATG
* * * * *
35501674 GAGGTATTT-TGATTATTTTATCCC-ATAGGGGTATTTCGGTCATTTTACCTTATG
1 GGGGTATTTCAG-TTATTTTA-CCCTATGGGGGTATTTTGGTCATTTTACCCTATG
* * * * *
35501728 AGGGTACTTT-GGTCATTTTACACTATGAGGGTATTTTGGTCATTTTACCC
1 GGGGTA-TTTCAGTTATTTTACCCTATGGGGGTATTTTGGTCATTTTACCC
35501778 ATTTTGGGGT
Statistics
Matches: 260, Mismatches: 54, Indels: 10
0.80 0.17 0.03
Matches are distributed among these distances:
53 47 0.18
54 206 0.79
55 7 0.03
ACGTcount: A:0.19, C:0.16, G:0.21, T:0.43
Consensus pattern (54 bp):
GGGGTATTTCAGTTATTTTACCCTATGGGGGTATTTTGGTCATTTTACCCTATG
Found at i:35501492 original size:81 final size:80
Alignment explanation
Indices: 35501415--35501777 Score: 397
Period size: 81 Copynumber: 4.5 Consensus size: 80
35501405 GGGGTATAAC
* * *
35501415 AGTCATTTTACCCTATAGGGGTATTTTGGTCATTCTACCGTCTGGGGGTATTTCGGTCATTCTAC
1 AGTCATTTTACCCTAT-GGGGTATTTTGGTCATTTTACCCTATGGGGGTATTTCGGTCATTCTAC
35501480 CCTATGGGGGTATTTT
65 CCTATGGGGGTATTTT
** * * * * *
35501496 AGTCATTTTACCCTATGGGGCTATTTCAGTTATTTTACCCTATGGGGGTATTTCGATTATTTTAT
1 AGTCATTTTACCCTATGGGG-TATTTTGGTCATTTTACCCTATGGGGGTATTTCGGTCATTCTAC
* *
35501561 CTTATGGGGGTATTTC
65 CCTATGGGGGTATTTT
* * * * *
35501577 AATTATTTTACCCTATGATGGTATTTCGGTCATTTTACCCTAT-GGGGTATTTCGGTTATTCTAC
1 AGTCATTTTACCCTATG-GGGTATTTTGGTCATTTTACCCTATGGGGGTATTTCGGTCATTCTAC
35501641 CCTATGGGGGTATTTT
65 CCTATGGGGGTATTTT
** * * * * *
35501657 TTTCATTCTACCCTATGGAGGTATTTTGATTATTTTATCCC-ATAGGGGTATTTCGGTCATTTTA
1 AGTCATTTTACCCTATGG-GGTATTTTGGTCATTTTA-CCCTATGGGGGTATTTCGGTCATTCTA
* * *
35501721 CCTTATGAGGGTACTTT
64 CCCTATGGGGGTATTTT
* *
35501738 GGTCATTTTACACTATGAGGGTATTTTGGTCATTTTACCC
1 AGTCATTTTACCCTATG-GGGTATTTTGGTCATTTTACCC
35501778 ATTTTGGGGT
Statistics
Matches: 235, Mismatches: 41, Indels: 13
0.81 0.14 0.04
Matches are distributed among these distances:
80 69 0.29
81 163 0.69
82 3 0.01
ACGTcount: A:0.18, C:0.17, G:0.21, T:0.44
Consensus pattern (80 bp):
AGTCATTTTACCCTATGGGGTATTTTGGTCATTTTACCCTATGGGGGTATTTCGGTCATTCTACC
CTATGGGGGTATTTT
Found at i:35502476 original size:12 final size:12
Alignment explanation
Indices: 35502459--35502500 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
35502449 ATTCCAATTT
35502459 TCTCTCCTCAAA
1 TCTCTCCTCAAA
*
35502471 TCTCT-CTAAATA
1 TCTCTCCTCAA-A
*
35502483 TCCCTCCTCAAA
1 TCTCTCCTCAAA
35502495 TCTCTC
1 TCTCTC
35502501 TATGACCAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
11 4 0.17
12 16 0.67
13 4 0.17
ACGTcount: A:0.24, C:0.40, G:0.00, T:0.36
Consensus pattern (12 bp):
TCTCTCCTCAAA
Found at i:35505632 original size:16 final size:16
Alignment explanation
Indices: 35505578--35505632 Score: 62
Period size: 16 Copynumber: 3.5 Consensus size: 16
35505568 TTTCTAAAAA
35505578 TAATATTATT-TTAATT
1 TAATATT-TTATTAATT
*
35505594 TAATATTTATATTGA--
1 TAATATTT-TATTAATT
35505609 TAATATTTTATTAATT
1 TAATATTTTATTAATT
35505625 TAATATTT
1 TAATATTT
35505633 ATGTGAGATA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
14 5 0.15
15 9 0.27
16 16 0.48
17 3 0.09
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (16 bp):
TAATATTTTATTAATT
Found at i:35505655 original size:30 final size:32
Alignment explanation
Indices: 35505577--35505687 Score: 108
Period size: 30 Copynumber: 3.7 Consensus size: 32
35505567 TTTTCTAAAA
* *
35505577 ATAATATT-ATTTTAATTTAATATTTATATTG
1 ATAATATTAAATTTAATTTAATATTTATAGTG
**
35505608 ATAATATTTTA-TTAATTTAATATTTAT-GTG
1 ATAATATTAAATTTAATTTAATATTTATAGTG
* **
35505638 A-GATATTAAATTTAATTTAATATTTATCTTG
1 ATAATATTAAATTTAATTTAATATTTATAGTG
*
35505669 ATAAGATT--ATTTAATTTAA
1 ATAATATTAAATTTAATTTAA
35505688 CATTAATGTG
Statistics
Matches: 67, Mismatches: 9, Indels: 9
0.79 0.11 0.11
Matches are distributed among these distances:
29 6 0.09
30 30 0.45
31 27 0.40
32 4 0.06
ACGTcount: A:0.40, C:0.01, G:0.05, T:0.54
Consensus pattern (32 bp):
ATAATATTAAATTTAATTTAATATTTATAGTG
Found at i:35505811 original size:30 final size:30
Alignment explanation
Indices: 35505776--35505867 Score: 89
Period size: 30 Copynumber: 3.1 Consensus size: 30
35505766 TTTCATACAC
*
35505776 AATATTTATATTATAATATTTTATTAATTT
1 AATATTTATATTATAATATTATATTAATTT
* * * *
35505806 AATATTTATGTGA-GATATTAAATTTAATTT
1 AATATTTATATTATAATATTATA-TTAATTT
* *
35505836 AATATTTATCTTGATAAGATTAT-TTAATTT
1 AATATTTATATT-ATAATATTATATTAATTT
35505866 AA
1 AA
35505868 CATTAATGTG
Statistics
Matches: 49, Mismatches: 10, Indels: 6
0.75 0.15 0.09
Matches are distributed among these distances:
29 6 0.12
30 37 0.76
31 1 0.02
32 5 0.10
ACGTcount: A:0.40, C:0.01, G:0.05, T:0.53
Consensus pattern (30 bp):
AATATTTATATTATAATATTATATTAATTT
Found at i:35505910 original size:180 final size:181
Alignment explanation
Indices: 35505595--35505955 Score: 715
Period size: 180 Copynumber: 2.0 Consensus size: 181
35505585 ATTTTAATTT
35505595 AATATTTATATTGATAATATTTTATTAATTTAATATTTATGTGAGATATTAAATTTAATTTAATA
1 AATATTTATATTGATAATATTTTATTAATTTAATATTTATGTGAGATATTAAATTTAATTTAATA
35505660 TTTATCTTGATAAGATTATTTAATTTAACATTAATGTGATTAATTCTAATCCTAGTTGAACTTCC
66 TTTATCTTGATAAGATTATTTAATTTAACATTAATGTGATTAATTCTAATCCTAGTTGAACTTCC
35505725 TCTAAACTCTCCCTATATAAAGAGAGAGTCTGGGCCATTATTTTCATACAC
131 TCTAAACTCTCCCTATATAAAGAGAGAGTCTGGGCCATTATTTTCATACAC
35505776 AATATTTATATT-ATAATATTTTATTAATTTAATATTTATGTGAGATATTAAATTTAATTTAATA
1 AATATTTATATTGATAATATTTTATTAATTTAATATTTATGTGAGATATTAAATTTAATTTAATA
35505840 TTTATCTTGATAAGATTATTTAATTTAACATTAATGTGATTAATTCTAATCCTAGTTGAACTTCC
66 TTTATCTTGATAAGATTATTTAATTTAACATTAATGTGATTAATTCTAATCCTAGTTGAACTTCC
35505905 TCTAAACTCTCCCTATATAAAGAGAGAGTCTGGGCCATTATTTTCATACAC
131 TCTAAACTCTCCCTATATAAAGAGAGAGTCTGGGCCATTATTTTCATACAC
35505956 TTGAATTCAA
Statistics
Matches: 180, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
180 168 0.93
181 12 0.07
ACGTcount: A:0.35, C:0.11, G:0.09, T:0.44
Consensus pattern (181 bp):
AATATTTATATTGATAATATTTTATTAATTTAATATTTATGTGAGATATTAAATTTAATTTAATA
TTTATCTTGATAAGATTATTTAATTTAACATTAATGTGATTAATTCTAATCCTAGTTGAACTTCC
TCTAAACTCTCCCTATATAAAGAGAGAGTCTGGGCCATTATTTTCATACAC
Found at i:35510602 original size:21 final size:22
Alignment explanation
Indices: 35510576--35510618 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
35510566 GGCTAGGTTT
*
35510576 TTTTAAT-TTTTAATGTTAGGG
1 TTTTAATATTTTAATGGTAGGG
35510597 TTTTAATATTTTAATGGTAGGG
1 TTTTAATATTTTAATGGTAGGG
35510619 CTAGAGTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.26, C:0.00, G:0.21, T:0.53
Consensus pattern (22 bp):
TTTTAATATTTTAATGGTAGGG
Found at i:35515944 original size:13 final size:13
Alignment explanation
Indices: 35515926--35515950 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
35515916 TGGTTAGCAA
35515926 CAGTTAGTCATAG
1 CAGTTAGTCATAG
35515939 CAGTTAGTCATA
1 CAGTTAGTCATA
35515951 CAAGTATAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (13 bp):
CAGTTAGTCATAG
Found at i:35521690 original size:30 final size:31
Alignment explanation
Indices: 35521651--35521710 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
35521641 AGAGGTGGGA
35521651 TGGGAAGGGAATAA-AAGTTTTAGGGGAAAAG
1 TGGGAAGGGAATAACAA-TTTTAGGGGAAAAG
* *
35521682 TGGG-AGGGAGTAACAATTTTGGGGGAAAA
1 TGGGAAGGGAATAACAATTTTAGGGGAAAA
35521711 TAAAAGGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 20 0.77
31 6 0.23
ACGTcount: A:0.38, C:0.02, G:0.40, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAACAATTTTAGGGGAAAAG
Found at i:35532107 original size:19 final size:19
Alignment explanation
Indices: 35532083--35532122 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
35532073 ATTATCTCTA
*
35532083 AATTTTAAAAATAATTTTT
1 AATTTTAAAAATAATGTTT
35532102 AATTTTAAAAATAATGTTT
1 AATTTTAAAAATAATGTTT
35532121 AA
1 AA
35532123 AATATTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (19 bp):
AATTTTAAAAATAATGTTT
Found at i:35532760 original size:18 final size:17
Alignment explanation
Indices: 35532737--35532780 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
35532727 GAAAAAAATC
35532737 ATTTAAATATTAATA-TAA
1 ATTTAAA-ATTAA-ACTAA
35532755 ATTTAAAATTAAACTAA
1 ATTTAAAATTAAACTAA
35532772 ATATTAAAA
1 AT-TTAAAA
35532781 ATAATAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 1 0.04
17 10 0.42
18 13 0.54
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (17 bp):
ATTTAAAATTAAACTAA
Found at i:35534639 original size:70 final size:70
Alignment explanation
Indices: 35534551--35534689 Score: 242
Period size: 70 Copynumber: 2.0 Consensus size: 70
35534541 GTGGATAGCT
* *
35534551 TTTGTTGCCTTTTTATATGTTATCCATGATTGTTTAAATGGATTAGATCGAGAATCGATTGATAT
1 TTTGTTACCTTTTTATATGTCATCCATGATTGTTTAAATGGATTAGATCGAGAATCGATTGATAT
35534616 ATCAC
66 ATCAC
* *
35534621 TTTGTTACCTTTTTATATGTCATCTATGGTTGTTTAAATGGATTAGATCGAGAATCGATTGATAT
1 TTTGTTACCTTTTTATATGTCATCCATGATTGTTTAAATGGATTAGATCGAGAATCGATTGATAT
35534686 ATCA
66 ATCA
35534690 ATTCGATGAG
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
70 65 1.00
ACGTcount: A:0.27, C:0.11, G:0.17, T:0.45
Consensus pattern (70 bp):
TTTGTTACCTTTTTATATGTCATCCATGATTGTTTAAATGGATTAGATCGAGAATCGATTGATAT
ATCAC
Found at i:35534912 original size:49 final size:49
Alignment explanation
Indices: 35534859--35534958 Score: 200
Period size: 49 Copynumber: 2.0 Consensus size: 49
35534849 TTTCTAAACC
35534859 AACCAGCCCAAATCCAAAAAATTGAATAAAAAGTACAACCCAAATAAAA
1 AACCAGCCCAAATCCAAAAAATTGAATAAAAAGTACAACCCAAATAAAA
35534908 AACCAGCCCAAATCCAAAAAATTGAATAAAAAGTACAACCCAAATAAAA
1 AACCAGCCCAAATCCAAAAAATTGAATAAAAAGTACAACCCAAATAAAA
35534957 AA
1 AA
35534959 ACAGAAAACT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.60, C:0.22, G:0.06, T:0.12
Consensus pattern (49 bp):
AACCAGCCCAAATCCAAAAAATTGAATAAAAAGTACAACCCAAATAAAA
Found at i:35535207 original size:18 final size:17
Alignment explanation
Indices: 35535184--35535222 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
35535174 AATATTTTTA
35535184 AAAAATAATAATTTAAAG
1 AAAAAT-ATAATTTAAAG
* *
35535202 AAAAATCTAATTTAAAT
1 AAAAATATAATTTAAAG
35535219 AAAA
1 AAAA
35535223 TTGTGGTCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.28
Consensus pattern (17 bp):
AAAAATATAATTTAAAG
Found at i:35538822 original size:3 final size:3
Alignment explanation
Indices: 35538814--35538849 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
35538804 TAGATAGCTT
35538814 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
35538850 TTGAATCTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
ATC
Found at i:35540033 original size:13 final size:13
Alignment explanation
Indices: 35540012--35540055 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
35540002 CCCCTAAAAA
35540012 TAATATTTTAATT
1 TAATATTTTAATT
* **
35540025 TAATCTTTTAAAAA
1 TAATATTTT-AATT
35540039 TAATATTTTAATT
1 TAATATTTTAATT
35540052 TAAT
1 TAAT
35540056 CTTTATCTTT
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
13 14 0.58
14 10 0.42
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (13 bp):
TAATATTTTAATT
Found at i:35540047 original size:14 final size:14
Alignment explanation
Indices: 35540006--35540049 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
35539996 TTTTGACCCC
35540006 TAAAAATAATATTT
1 TAAAAATAATATTT
** *
35540020 T-AATTTAATCTTT
1 TAAAAATAATATTT
35540033 TAAAAATAATATTT
1 TAAAAATAATATTT
35540047 TAA
1 TAA
35540050 TTTAATCTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
13 10 0.43
14 13 0.57
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (14 bp):
TAAAAATAATATTT
Found at i:35540057 original size:27 final size:27
Alignment explanation
Indices: 35540006--35540059 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
35539996 TTTTGACCCC
35540006 TAAAAATAATATTTTAATTTAATCTTT
1 TAAAAATAATATTTTAATTTAATCTTT
35540033 TAAAAATAATATTTTAATTTAATCTTT
1 TAAAAATAATATTTTAATTTAATCTTT
35540060 ATCTTTTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (27 bp):
TAAAAATAATATTTTAATTTAATCTTT
Found at i:35544624 original size:13 final size:13
Alignment explanation
Indices: 35544606--35544648 Score: 52
Period size: 14 Copynumber: 3.2 Consensus size: 13
35544596 CAGAAGAGTA
35544606 TTATTATTTATTT
1 TTATTATTTATTT
35544619 TTATTATGTTATTAT
1 TTATTAT-TTATT-T
35544634 TT-TATATTTATTT
1 TTAT-TATTTATTT
35544647 TT
1 TT
35544649 TTGCATTCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
13 10 0.37
14 11 0.41
15 6 0.22
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.74
Consensus pattern (13 bp):
TTATTATTTATTT
Found at i:35546883 original size:22 final size:21
Alignment explanation
Indices: 35546840--35546896 Score: 71
Period size: 22 Copynumber: 2.7 Consensus size: 21
35546830 TGTAGTTTTC
35546840 TAGGTGAAAAGTTGGATGTGA
1 TAGGTGAAAAGTTGGATGTGA
*
35546861 TAGGTGAAATA-TTAGGATTTGA
1 TAGGTGAAA-AGTT-GGATGTGA
*
35546883 TAGGTGAAAGGTTG
1 TAGGTGAAAAGTTG
35546897 ATGGGTATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
21 12 0.39
22 19 0.61
ACGTcount: A:0.33, C:0.00, G:0.35, T:0.32
Consensus pattern (21 bp):
TAGGTGAAAAGTTGGATGTGA
Found at i:35555250 original size:18 final size:18
Alignment explanation
Indices: 35555229--35555264 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
35555219 ACCCTGTCTG
35555229 TGATAATTTCATATCATT
1 TGATAATTTCATATCATT
35555247 TGATAATTTCATATCATT
1 TGATAATTTCATATCATT
35555265 GTAAAATTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.11, G:0.06, T:0.50
Consensus pattern (18 bp):
TGATAATTTCATATCATT
Found at i:35555272 original size:18 final size:18
Alignment explanation
Indices: 35555233--35555273 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
35555223 TGTCTGTGAT
*
35555233 AATTTCATATCATTTGAT
1 AATTTCATATCATTTGAA
35555251 AATTTCATATCA-TTGTAA
1 AATTTCATATCATTTG-AA
35555269 AATTT
1 AATTT
35555274 GAAATGAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 3 0.14
18 18 0.86
ACGTcount: A:0.37, C:0.10, G:0.05, T:0.49
Consensus pattern (18 bp):
AATTTCATATCATTTGAA
Found at i:35555339 original size:15 final size:15
Alignment explanation
Indices: 35555319--35555356 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
35555309 AAATATTTAT
35555319 GTTTAAACCTTTAGA
1 GTTTAAACCTTTAGA
*
35555334 GTTTAAACCTTTATA
1 GTTTAAACCTTTAGA
35555349 GTTGTAAA
1 GTT-TAAA
35555357 GTTGTTTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 17 0.81
16 4 0.19
ACGTcount: A:0.34, C:0.11, G:0.13, T:0.42
Consensus pattern (15 bp):
GTTTAAACCTTTAGA
Found at i:35560047 original size:6 final size:6
Alignment explanation
Indices: 35560036--35560060 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
35560026 CATTATCAAC
35560036 ATATAA ATATAA ATATAA ATATAA A
1 ATATAA ATATAA ATATAA ATATAA A
35560061 AGGGAAAAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
ATATAA
Found at i:35562018 original size:43 final size:42
Alignment explanation
Indices: 35561948--35562063 Score: 112
Period size: 41 Copynumber: 2.8 Consensus size: 42
35561938 TATAAAGCTC
* * * * *
35561948 ATACAATGCCATATCCCAGATATGGTCTTACATGCTAACGCAT
1 ATACGATGCCATGTCCCAGACATGGTCTTACATACGAA-GCAT
* *
35561991 AT-CGATGCCACTGTCCCAGACAGGGTCTT--ATACGAATCAT
1 ATACGATGCCA-TGTCCCAGACATGGTCTTACATACGAAGCAT
*
35562031 ATATGATGCCAATGTCCCAGACATGGTCTTACA
1 ATACGATGCC-ATGTCCCAGACATGGTCTTACA
35562064 CGAAATCACA
Statistics
Matches: 59, Mismatches: 9, Indels: 10
0.76 0.12 0.13
Matches are distributed among these distances:
40 5 0.08
41 28 0.47
42 8 0.14
43 18 0.31
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (42 bp):
ATACGATGCCATGTCCCAGACATGGTCTTACATACGAAGCAT
Found at i:35562049 original size:41 final size:42
Alignment explanation
Indices: 35561989--35562067 Score: 124
Period size: 41 Copynumber: 1.9 Consensus size: 42
35561979 ATGCTAACGC
* *
35561989 ATATCGATGCCACTGTCCCAGACAGGGTCTTATACGAATCAT
1 ATATCGATGCCAATGTCCCAGACAGGGTCTTACACGAATCAT
*
35562031 ATAT-GATGCCAATGTCCCAGACATGGTCTTACACGAA
1 ATATCGATGCCAATGTCCCAGACAGGGTCTTACACGAA
35562068 ATCACACCTC
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
41 30 0.88
42 4 0.12
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.25
Consensus pattern (42 bp):
ATATCGATGCCAATGTCCCAGACAGGGTCTTACACGAATCAT
Found at i:35562283 original size:61 final size:62
Alignment explanation
Indices: 35562188--35562543 Score: 417
Period size: 61 Copynumber: 5.9 Consensus size: 62
35562178 ATCCAATACT
* * *
35562188 CAAATC-AATTCGACAAT-TAATATCCATATACAAATTAAATTCGGCAATGTATATCTATATA
1 CAAATCAAATTCGGCAATGT-ATATCTATATACAAATCAAATTCGGCAATGTATATCTATATA
* * *
35562249 CAAATC-AATACGGCAATGAATATCTATATACAAATCAAATTCGGCAATGTATA-CCATATA
1 CAAATCAAATTCGGCAATGTATATCTATATACAAATCAAATTCGGCAATGTATATCTATATA
* * * *
35562309 TAAATCAAATTCGGCAATGTATATCTATATTCAAATCAAATTCGGCAATGTATAACCATATA
1 CAAATCAAATTCGGCAATGTATATCTATATACAAATCAAATTCGGCAATGTATATCTATATA
* * *
35562371 CAAATCAAATTCGGCAATGTATAACCATATACAAATCAAATTTGGCAA---ATATCTATATA
1 CAAATCAAATTCGGCAATGTATATCTATATACAAATCAAATTCGGCAATGTATATCTATATA
* * * * ** *
35562430 CAAATC-ACTTCGGCAATGTATATTTATAAACAAATCAATTTCGATAATGTATATCTATAAA
1 CAAATCAAATTCGGCAATGTATATCTATATACAAATCAAATTCGGCAATGTATATCTATATA
** *
35562491 CAAATCAAATTTAGCAATGTATATCTTTATACAAATC-AATT-GGACAATGTATA
1 CAAATCAAATTCGGCAATGTATATCTATATACAAATCAAATTCGG-CAATGTATA
35562544 AAACATATAC
Statistics
Matches: 251, Mismatches: 36, Indels: 16
0.83 0.12 0.05
Matches are distributed among these distances:
58 32 0.13
59 15 0.06
60 12 0.05
61 118 0.47
62 74 0.29
ACGTcount: A:0.44, C:0.16, G:0.09, T:0.31
Consensus pattern (62 bp):
CAAATCAAATTCGGCAATGTATATCTATATACAAATCAAATTCGGCAATGTATATCTATATA
Found at i:35562481 original size:120 final size:123
Alignment explanation
Indices: 35562188--35562529 Score: 399
Period size: 120 Copynumber: 2.8 Consensus size: 123
35562178 ATCCAATACT
* * * * *
35562188 CAAATC-AATTCGACAAT-TAATATCCATATACAAATTAAATTCGGCAATGTATATCTATATACA
1 CAAATCAAATTCGGCAATGT-ATATCTATAAACAAATCAAATTCGACAATGTATATCTATATACA
* * *
35562251 AATC-AATACGGCAATGAATATCTATATACAAATCAAATTCGGCAATGTATACCATATA
65 AATCAAATTCGGCAATGTATATCTATATACAAATCAAATTCGGCAATATATACCATATA
* ** * * *
35562309 TAAATCAAATTCGGCAATGTATATCTATATTCAAATCAAATTCGGCAATGTATAACCATATACAA
1 CAAATCAAATTCGGCAATGTATATCTATAAACAAATCAAATTCGACAATGTATATCTATATACAA
* * * *
35562374 ATCAAATTCGGCAATGTATAACCATATACAAATCAAATTTGGCAA-ATAT-CTATATA
66 ATCAAATTCGGCAATGTATATCTATATACAAATCAAATTCGGCAATATATACCATATA
* * * * *
35562430 CAAATC-ACTTCGGCAATGTATATTTATAAACAAATCAATTTCGATAATGTATATCTATAAACAA
1 CAAATCAAATTCGGCAATGTATATCTATAAACAAATCAAATTCGACAATGTATATCTATATACAA
** *
35562494 ATCAAATTTAGCAATGTATATCTTTATACAAATCAA
66 ATCAAATTCGGCAATGTATATCTATATACAAATCAA
35562530 TTGGACAATG
Statistics
Matches: 188, Mismatches: 30, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
120 79 0.42
121 16 0.09
122 56 0.30
123 37 0.20
ACGTcount: A:0.44, C:0.16, G:0.08, T:0.31
Consensus pattern (123 bp):
CAAATCAAATTCGGCAATGTATATCTATAAACAAATCAAATTCGACAATGTATATCTATATACAA
ATCAAATTCGGCAATGTATATCTATATACAAATCAAATTCGGCAATATATACCATATA
Found at i:35562498 original size:151 final size:152
Alignment explanation
Indices: 35562188--35562554 Score: 433
Period size: 151 Copynumber: 2.4 Consensus size: 152
35562178 ATCCAATACT
* * * *
35562188 CAAATC-AATTCGACAAT-TAATATCCATATACAAATTAAATTCGGCAATGTATATCTATATACA
1 CAAATCAAATTCGGCAATGT-ATATCCATATACAAATCAAATTCGGCAATGTATAACCATATACA
* *
35562251 AATCAATACGGCAATGAATATCTATATACAAATCAAATTCGGCAATGTATACCATATATAAATCA
65 AATCAATACGGCAA-GAATATCTATATACAAATCAAATTCGGCAATGTATACCATAAACAAATCA
* **
35562316 AATTCGGCAATGTATATCTATATT
129 AATTCGACAATGTATATCTATAAA
*
35562340 CAAATCAAATTCGGCAATGTATAACCATATACAAATCAAATTCGGCAATGTATAACCATATACAA
1 CAAATCAAATTCGGCAATGTATATCCATATACAAATCAAATTCGGCAATGTATAACCATATACAA
** * **
35562405 ATCAAATTTGGC-A-AATATCTATATACAAATC-ACTTCGGCAATGTATATTTATAAACAAATCA
66 ATC-AATACGGCAAGAATATCTATATACAAATCAAATTCGGCAATGTATA-CCATAAACAAATCA
* *
35562467 ATTTCGATAATGTATATCTATAAA
129 AATTCGACAATGTATATCTATAAA
** ** *
35562491 CAAATCAAATTTAGCAATGTATATCTTTATACAAATC-AATT-GGACAATGTATAAAACATATAC
1 CAAATCAAATTCGGCAATGTATATCCATATACAAATCAAATTCGG-CAATGTAT-AACCATATAC
35562554 A
64 A
35562555 TTTAATTTCA
Statistics
Matches: 186, Mismatches: 23, Indels: 13
0.84 0.10 0.06
Matches are distributed among these distances:
149 2 0.01
150 27 0.15
151 89 0.48
152 6 0.03
153 55 0.30
154 7 0.04
ACGTcount: A:0.44, C:0.16, G:0.08, T:0.31
Consensus pattern (152 bp):
CAAATCAAATTCGGCAATGTATATCCATATACAAATCAAATTCGGCAATGTATAACCATATACAA
ATCAATACGGCAAGAATATCTATATACAAATCAAATTCGGCAATGTATACCATAAACAAATCAAA
TTCGACAATGTATATCTATAAA
Found at i:35562541 original size:30 final size:31
Alignment explanation
Indices: 35562188--35562543 Score: 417
Period size: 31 Copynumber: 11.7 Consensus size: 31
35562178 ATCCAATACT
* *
35562188 CAAATC-AATTCGACAAT-TAATATCCATATA
1 CAAATCAAATTCGGCAATGT-ATATCTATATA
*
35562218 CAAATTAAATTCGGCAATGTATATCTATATA
1 CAAATCAAATTCGGCAATGTATATCTATATA
* *
35562249 CAAATC-AATACGGCAATGAATATCTATATA
1 CAAATCAAATTCGGCAATGTATATCTATATA
*
35562279 CAAATCAAATTCGGCAATGTATA-CCATATA
1 CAAATCAAATTCGGCAATGTATATCTATATA
* *
35562309 TAAATCAAATTCGGCAATGTATATCTATATT
1 CAAATCAAATTCGGCAATGTATATCTATATA
* *
35562340 CAAATCAAATTCGGCAATGTATAACCATATA
1 CAAATCAAATTCGGCAATGTATATCTATATA
* *
35562371 CAAATCAAATTCGGCAATGTATAACCATATA
1 CAAATCAAATTCGGCAATGTATATCTATATA
*
35562402 CAAATCAAATTTGGCAA---ATATCTATATA
1 CAAATCAAATTCGGCAATGTATATCTATATA
* * *
35562430 CAAATC-ACTTCGGCAATGTATATTTATAAA
1 CAAATCAAATTCGGCAATGTATATCTATATA
* ** *
35562460 CAAATCAATTTCGATAATGTATATCTATAAA
1 CAAATCAAATTCGGCAATGTATATCTATATA
** *
35562491 CAAATCAAATTTAGCAATGTATATCTTTATA
1 CAAATCAAATTCGGCAATGTATATCTATATA
35562522 CAAATC-AATT-GGACAATGTATA
1 CAAATCAAATTCGG-CAATGTATA
35562544 AAACATATAC
Statistics
Matches: 282, Mismatches: 35, Indels: 18
0.84 0.10 0.05
Matches are distributed among these distances:
27 8 0.03
28 15 0.05
29 1 0.00
30 89 0.32
31 168 0.60
32 1 0.00
ACGTcount: A:0.44, C:0.16, G:0.09, T:0.31
Consensus pattern (31 bp):
CAAATCAAATTCGGCAATGTATATCTATATA
Found at i:35568894 original size:125 final size:123
Alignment explanation
Indices: 35568669--35568953 Score: 385
Period size: 125 Copynumber: 2.3 Consensus size: 123
35568659 TATATATCCA
* * * * *
35568669 TATACGAATCAAATTCGGCAATGTATATCTATATACAAATCAATTTGGCAATGAATATCTATATA
1 TATACAAATCAAATTCGGCAATGTATAACCATATACAAATCAATTCGGCAATGAATATCTATAAA
* *
35568734 CAAATCAAATTCGGCAATGTATATCTATATACAAATCAAATTCTG-CAATGTATAACTG
66 AAAATCAAATTCGGCAATGTATATCTATAAACAAATCAAATTC-GACAATGTATAACTG
* * *
35568792 TATACAGATCAAATTCAGCAATGTATAACCATATACAAATCAAATTCGGCAATGTATATCTATAA
1 TATACAAATCAAATTCGGCAATGTATAACCATATACAAATC-AATTCGGCAATGAATATCTAT-A
* * * *
35568857 AAAAAATCAATTTCGGTAATGTATATCTATAAACAAATCAAATTCGACAATGTATATCTT
64 AAAAAATCAAATTCGGCAATGTATATCTATAAACAAATCAAATTCGACAATGTATAACTG
*
35568917 TATACAAATC-AATTCGGCAATGTATAAAACATATACA
1 TATACAAATCAAATTCGGCAATGTAT-AACCATATACA
35568954 TTTAATTTCA
Statistics
Matches: 141, Mismatches: 17, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
123 36 0.26
124 34 0.24
125 71 0.50
ACGTcount: A:0.44, C:0.15, G:0.09, T:0.31
Consensus pattern (123 bp):
TATACAAATCAAATTCGGCAATGTATAACCATATACAAATCAATTCGGCAATGAATATCTATAAA
AAAATCAAATTCGGCAATGTATATCTATAAACAAATCAAATTCGACAATGTATAACTG
Found at i:35568953 original size:31 final size:31
Alignment explanation
Indices: 35568641--35568942 Score: 385
Period size: 31 Copynumber: 9.7 Consensus size: 31
35568631 ATCCAATACT
* *
35568641 CAAATCAAATT-GGCAATATATATATCCATATA
1 CAAATCAAATTCGGC-A-ATGTATATCTATATA
*
35568673 CGAATCAAATTCGGCAATGTATATCTATATA
1 CAAATCAAATTCGGCAATGTATATCTATATA
* *
35568704 CAAATC-AATTTGGCAATGAATATCTATATA
1 CAAATCAAATTCGGCAATGTATATCTATATA
35568734 CAAATCAAATTCGGCAATGTATATCTATATA
1 CAAATCAAATTCGGCAATGTATATCTATATA
* * *
35568765 CAAATCAAATTCTGCAATGTATAACTGTATA
1 CAAATCAAATTCGGCAATGTATATCTATATA
* * * *
35568796 CAGATCAAATTCAGCAATGTATAACCATATA
1 CAAATCAAATTCGGCAATGTATATCTATATA
*
35568827 CAAATCAAATTCGGCAATGTATATCTATAAAA
1 CAAATCAAATTCGGCAATGTATATCTAT-ATA
* * * *
35568859 AAAATCAATTTCGGTAATGTATATCTATAAA
1 CAAATCAAATTCGGCAATGTATATCTATATA
* *
35568890 CAAATCAAATTCGACAATGTATATCTTTATA
1 CAAATCAAATTCGGCAATGTATATCTATATA
35568921 CAAATC-AATTCGGCAATGTATA
1 CAAATCAAATTCGGCAATGTATA
35568943 AAACATATAC
Statistics
Matches: 237, Mismatches: 30, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
30 43 0.18
31 153 0.65
32 38 0.16
33 3 0.01
ACGTcount: A:0.43, C:0.16, G:0.10, T:0.31
Consensus pattern (31 bp):
CAAATCAAATTCGGCAATGTATATCTATATA
Found at i:35570951 original size:20 final size:20
Alignment explanation
Indices: 35570923--35570968 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
35570913 ATTGATTTTG
*
35570923 TATTTTTTTTA-AAAATTCAA
1 TATTATTTTTATAAAATTC-A
*
35570943 TATTATTTTTATTAAATTCA
1 TATTATTTTTATAAAATTCA
35570963 TATTAT
1 TATTAT
35570969 ATCATAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 17 0.74
21 6 0.26
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (20 bp):
TATTATTTTTATAAAATTCA
Found at i:35577735 original size:18 final size:18
Alignment explanation
Indices: 35577714--35577757 Score: 72
Period size: 18 Copynumber: 2.4 Consensus size: 18
35577704 CATAATAACA
35577714 AAAATTATAAAATAAAAT-
1 AAAATTATAAAA-AAAATC
35577732 AAAATTATAAAAAAAATC
1 AAAATTATAAAAAAAATC
35577750 AAAATTAT
1 AAAATTAT
35577758 TCATAAAAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
17 5 0.20
18 20 0.80
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.27
Consensus pattern (18 bp):
AAAATTATAAAAAAAATC
Found at i:35578911 original size:23 final size:23
Alignment explanation
Indices: 35578867--35578913 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
35578857 TTATAAAATC
* *
35578867 AAATTAAATTATAAACAGATAAA
1 AAATTAAAATATAAACAAATAAA
**
35578890 AAATTAAAATATAATTAAATAAA
1 AAATTAAAATATAAACAAATAAA
35578913 A
1 A
35578914 CTCACACATA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.28
Consensus pattern (23 bp):
AAATTAAAATATAAACAAATAAA
Found at i:35581649 original size:10 final size:11
Alignment explanation
Indices: 35581631--35581674 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
35581621 TTAATAAGAT
35581631 TTAATATTAAA
1 TTAATATTAAA
35581642 TTAA-ATTAAA
1 TTAATATTAAA
* *
35581652 TATTATATTAAT
1 T-TAATATTAAA
35581664 TTAATATTAAA
1 TTAATATTAAA
35581675 ATGATTAAGT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
10 7 0.26
11 14 0.52
12 6 0.22
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
TTAATATTAAA
Found at i:35581655 original size:17 final size:16
Alignment explanation
Indices: 35581633--35581674 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
35581623 AATAAGATTT
35581633 AATATTAAATTAAATTA
1 AATATTAAATT-AATTA
* *
35581650 AATATTATATTAATTT
1 AATATTAAATTAATTA
35581666 AATATTAAA
1 AATATTAAA
35581675 ATGATTAAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
16 12 0.55
17 10 0.45
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AATATTAAATTAATTA
Found at i:35588189 original size:19 final size:21
Alignment explanation
Indices: 35588148--35588190 Score: 54
Period size: 19 Copynumber: 2.1 Consensus size: 21
35588138 TTTTTAGAAA
* *
35588148 AAAAAAACAAAGGTGAAACAG
1 AAAAAAACAAAGCTGAAAAAG
35588169 AAAAAAA-AAAGCT-AAAAAG
1 AAAAAAACAAAGCTGAAAAAG
35588188 AAA
1 AAA
35588191 CCGTTGAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 8 0.40
20 5 0.25
21 7 0.35
ACGTcount: A:0.74, C:0.07, G:0.14, T:0.05
Consensus pattern (21 bp):
AAAAAAACAAAGCTGAAAAAG
Found at i:35588762 original size:70 final size:69
Alignment explanation
Indices: 35588562--35588764 Score: 203
Period size: 71 Copynumber: 2.9 Consensus size: 69
35588552 GGGAGTATGA
* * * **
35588562 AATTCCCATTAATTTTTTTTTCTTTTAAATAATTTTTGAAAAAGTTGTTTCCAA-TTATAAAAAT
1 AATTCCCATTAAATATTTTTTCCTTTAAAT-ATTTTT-AAAAAGTTGTCACCAACTT-TAAAAAT
**
35588626 TTCATTT
63 CCCATTT
* * * * **
35588633 AATTCCCATCATATATTTTTTTCCTTTACATATACTTTTAAAAAG-TATCAGAAACTTTAAAAAT
1 AATTCCCATTAAATA-TTTTTTCCTTTA-A-ATATTTTTAAAAAGTTGTCACCAACTTTAAAAAT
35588697 CCCATTT
63 CCCATTT
*
35588704 AATTCCCATTAAATATTTTTTCCTTTAAATATTTATTTAAAAGTTGTCACCAACTTTAAAA
1 AATTCCCATTAAATATTTTTTCCTTTAAATATTT-TTAAAAAGTTGTCACCAACTTTAAAA
35588765 TAAATATAGT
Statistics
Matches: 106, Mismatches: 20, Indels: 13
0.76 0.14 0.09
Matches are distributed among these distances:
68 5 0.05
69 8 0.08
70 26 0.25
71 40 0.38
72 19 0.18
73 6 0.06
74 2 0.02
ACGTcount: A:0.36, C:0.14, G:0.03, T:0.46
Consensus pattern (69 bp):
AATTCCCATTAAATATTTTTTCCTTTAAATATTTTTAAAAAGTTGTCACCAACTTTAAAAATCCC
ATTT
Found at i:35588891 original size:23 final size:23
Alignment explanation
Indices: 35588861--35588915 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
35588851 GTCACCAACT
*
35588861 TTAAAATTCCCATTTAATT-TCTA
1 TTAAAATTCCCATCTAATTCTC-A
*
35588884 TTAAAATTCTCATCTAATTCTCA
1 TTAAAATTCCCATCTAATTCTCA
35588907 TTAAAATTC
1 TTAAAATTC
35588916 ACATAACTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 27 0.93
24 2 0.07
ACGTcount: A:0.36, C:0.18, G:0.00, T:0.45
Consensus pattern (23 bp):
TTAAAATTCCCATCTAATTCTCA
Found at i:35588893 original size:11 final size:12
Alignment explanation
Indices: 35588861--35588915 Score: 53
Period size: 11 Copynumber: 4.8 Consensus size: 12
35588851 GTCACCAACT
*
35588861 TTAAAATTCCCA
1 TTAAAATTCTCA
* *
35588873 TTTAATTTCT-A
1 TTAAAATTCTCA
35588884 TTAAAATTCTCA
1 TTAAAATTCTCA
35588896 TCT--AATTCTCA
1 T-TAAAATTCTCA
35588907 TTAAAATTC
1 TTAAAATTC
35588916 ACATAACTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
10 1 0.03
11 18 0.53
12 14 0.41
13 1 0.03
ACGTcount: A:0.36, C:0.18, G:0.00, T:0.45
Consensus pattern (12 bp):
TTAAAATTCTCA
Found at i:35590046 original size:12 final size:12
Alignment explanation
Indices: 35590022--35590053 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
35590012 TTTTCATTTA
35590022 TTTTCTTTCT-T
1 TTTTCTTTCTGT
35590033 TTTT-TTTCTGT
1 TTTTCTTTCTGT
35590044 TTTTCTTTCT
1 TTTTCTTTCT
35590054 CTTCTTTTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
10 5 0.26
11 9 0.47
12 5 0.26
ACGTcount: A:0.00, C:0.16, G:0.03, T:0.81
Consensus pattern (12 bp):
TTTTCTTTCTGT
Found at i:35602638 original size:51 final size:50
Alignment explanation
Indices: 35602580--35602749 Score: 173
Period size: 51 Copynumber: 3.4 Consensus size: 50
35602570 TTTTGGGGTT
* * * *
35602580 TTCACATAGTACCACCCATGTTACTATTATCATTCGATACACGTAGTAGCC
1 TTCACATAGTACTACACATGTGACAATTATC-TTCGATACACGTAGTAGCC
* * *
35602631 TTCACATAGTACTACACACGTGATCAAGTT-T-TACGATCCACGTAGTAGCC
1 TTCACATAGTACTACACATGTGA-CAA-TTATCTTCGATACACGTAGTAGCC
*** * * *
35602681 TTCACATAGTACTACACATGTGACCAAAGCTTTTTGGTACACGTAGTAGCC
1 TTCACATAGTACTACACATGTGA-CAATTATCTTCGATACACGTAGTAGCC
35602732 TTCACATAGTACTACACA
1 TTCACATAGTACTACACA
35602750 CGTGTTCATC
Statistics
Matches: 100, Mismatches: 15, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
50 43 0.43
51 52 0.52
52 3 0.03
53 2 0.02
ACGTcount: A:0.31, C:0.26, G:0.14, T:0.29
Consensus pattern (50 bp):
TTCACATAGTACTACACATGTGACAATTATCTTCGATACACGTAGTAGCC
Found at i:35602680 original size:50 final size:51
Alignment explanation
Indices: 35602612--35602753 Score: 216
Period size: 50 Copynumber: 2.8 Consensus size: 51
35602602 ACTATTATCA
*
35602612 TTCGATACACGTAGTAGCCTTCACATAGTACTACACACGTGATC-AAG-TT
1 TTCGATACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGCTT
* *
35602661 TTACGATCCACGTAGTAGCCTTCACATAGTACTACACATGTGACCAAAGCTT
1 TT-CGATACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGCTT
* *
35602713 TTTGGTACACGTAGTAGCCTTCACATAGTACTACACACGTG
1 TTCGATACACGTAGTAGCCTTCACATAGTACTACACACGTG
35602754 TTCATCGATA
Statistics
Matches: 83, Mismatches: 7, Indels: 4
0.88 0.07 0.04
Matches are distributed among these distances:
49 2 0.02
50 39 0.47
51 38 0.46
52 4 0.05
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (51 bp):
TTCGATACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGCTT
Found at i:35614454 original size:24 final size:26
Alignment explanation
Indices: 35614427--35614475 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 26
35614417 GGGGAGTAAA
*
35614427 AAAAAGAAGAAG-AA-AAGAGAAAAC
1 AAAAAGAAAAAGAAAGAAGAGAAAAC
*
35614451 AAAAATAAAAAGAAAGAAGAGAAAA
1 AAAAAGAAAAAGAAAGAAGAGAAAA
35614476 AGAATGAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 10 0.48
25 2 0.10
26 9 0.43
ACGTcount: A:0.78, C:0.02, G:0.18, T:0.02
Consensus pattern (26 bp):
AAAAAGAAAAAGAAAGAAGAGAAAAC
Found at i:35614468 original size:28 final size:26
Alignment explanation
Indices: 35614424--35614476 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 26
35614414 AACGGGGAGT
35614424 AAAAAAAAGAAGAAGAAAAGAGAAAAC
1 AAAAAAAAGAAGAAGAAAAGA-AAAAC
*
35614451 AAAAATAAA-AAGAAAGAAGAGAAAAA
1 AAAAA-AAAGAAG-AAGAAAAGAAAAA
35614477 GAATGAAACC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
27 12 0.52
28 11 0.48
ACGTcount: A:0.79, C:0.02, G:0.17, T:0.02
Consensus pattern (26 bp):
AAAAAAAAGAAGAAGAAAAGAAAAAC
Found at i:35614470 original size:26 final size:27
Alignment explanation
Indices: 35614424--35614475 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
35614414 AACGGGGAGT
35614424 AAAAAAAAGAAGAAGAAAAGAGAAAAC
1 AAAAAAAAGAAGAAGAAAAGAGAAAAC
*
35614451 AAAAATAAA-AAGAA-AGAAGAGAAAA
1 AAAAA-AAAGAAGAAGAAAAGAGAAAA
35614476 AGAATGAAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 10 0.43
27 10 0.43
28 3 0.13
ACGTcount: A:0.79, C:0.02, G:0.17, T:0.02
Consensus pattern (27 bp):
AAAAAAAAGAAGAAGAAAAGAGAAAAC
Found at i:35626179 original size:41 final size:41
Alignment explanation
Indices: 35626134--35626239 Score: 104
Period size: 41 Copynumber: 2.6 Consensus size: 41
35626124 ATCCTACTTG
* * * *
35626134 GCTCAAAGCTCGACACGATACACCAGTACGAAGACTTCTAA
1 GCTCAAAGCACGACACAATACACCAGCACGAAGACTACTAA
* * * * *
35626175 GCTCAAGGCACGATACAATACACCGGCACGAAGCCTACTAG
1 GCTCAAAGCACGACACAATACACCAGCACGAAGACTACTAA
* * *
35626216 GCTCAAAGCCCGATATAATACACC
1 GCTCAAAGCACGACACAATACACC
35626240 CAACACATTT
Statistics
Matches: 53, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.36, C:0.31, G:0.18, T:0.15
Consensus pattern (41 bp):
GCTCAAAGCACGACACAATACACCAGCACGAAGACTACTAA
Found at i:35629689 original size:5 final size:5
Alignment explanation
Indices: 35629675--35629745 Score: 67
Period size: 5 Copynumber: 14.2 Consensus size: 5
35629665 CATGGGAAAT
*
35629675 TTTTC CTTTC TTTTC TTTTC TTTTC TTTTC -TTTC -TTTC -TTTC TTCCTTCC
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TT--TT-C
* *
35629725 TTTTT TTTTC TTTTC CTTTC T
1 TTTTC TTTTC TTTTC TTTTC T
35629746 CCCCCCTTTA
Statistics
Matches: 56, Mismatches: 6, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
4 12 0.21
5 37 0.66
6 2 0.04
7 2 0.04
8 3 0.05
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (5 bp):
TTTTC
Found at i:35640597 original size:8 final size:7
Alignment explanation
Indices: 35640572--35640602 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
35640562 CGAAAAGAAA
35640572 AAAAAAG
1 AAAAAAG
35640579 AAAAAAG
1 AAAAAAG
35640586 AAAAAAG
1 AAAAAAG
*
35640593 CAAAAAG
1 AAAAAAG
35640600 AAA
1 AAA
35640603 TAAAATCTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.84, C:0.03, G:0.13, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:35640756 original size:9 final size:9
Alignment explanation
Indices: 35640720--35640752 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
35640710 TAAAAATAAT
35640720 AATAAGAAA
1 AATAAGAAA
35640729 AATAAGAAA
1 AATAAGAAA
35640738 AATAA-ATAA
1 AATAAGA-AA
35640747 AATAAG
1 AATAAG
35640753 TAAATGAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 1 0.05
9 21 0.95
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (9 bp):
AATAAGAAA
Found at i:35648705 original size:30 final size:30
Alignment explanation
Indices: 35648664--35648732 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
35648654 AGTAGCACAC
35648664 GACCATGTGGACCGCCCATGTGCGGAACAT
1 GACCATGTGGACCGCCCATGTGCGGAACAT
* * * * *
35648694 GACCGTGTGGACTGCCCGTGTGTGGCACAT
1 GACCATGTGGACCGCCCATGTGCGGAACAT
*
35648724 GCCCATGTG
1 GACCATGTG
35648733 CAAAACCACC
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.17, C:0.29, G:0.33, T:0.20
Consensus pattern (30 bp):
GACCATGTGGACCGCCCATGTGCGGAACAT
Found at i:35657336 original size:6 final size:6
Alignment explanation
Indices: 35657325--35657351 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
35657315 TAAAAAAATA
35657325 AATTAT AATTAT AATTAT AATTAT AAT
1 AATTAT AATTAT AATTAT AATTAT AAT
35657352 GATTTATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
AATTAT
Found at i:35658379 original size:15 final size:16
Alignment explanation
Indices: 35658359--35658393 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
35658349 TTAAACAAGG
35658359 TTAAAGATTAATT-AA
1 TTAAAGATTAATTAAA
*
35658374 TTAAAGTTTAATTAAA
1 TTAAAGATTAATTAAA
35658390 TTAA
1 TTAA
35658394 TTAAGGTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (16 bp):
TTAAAGATTAATTAAA
Found at i:35658403 original size:19 final size:20
Alignment explanation
Indices: 35658368--35658407 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
35658358 GTTAAAGATT
*
35658368 AATTAATTAAAGTTTAATTA
1 AATTAATTAAAGGTTAATTA
35658388 AATTAATT-AAGGTTAATTA
1 AATTAATTAAAGGTTAATTA
35658407 A
1 A
35658408 CTTATAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.42
Consensus pattern (20 bp):
AATTAATTAAAGGTTAATTA
Found at i:35658425 original size:11 final size:10
Alignment explanation
Indices: 35658370--35658421 Score: 52
Period size: 11 Copynumber: 5.1 Consensus size: 10
35658360 TAAAGATTAA
35658370 TTAATTAAAG
1 TTAATTAAAG
35658380 TTTAATTAAA-
1 -TTAATTAAAG
*
35658390 TTAATTAAGG
1 TTAATTAAAG
**
35658400 TTAATTAACT
1 TTAATTAAAG
35658410 TATAATTAAAG
1 T-TAATTAAAG
35658421 T
1 T
35658422 ATAAAAGATA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
9 8 0.24
10 9 0.26
11 17 0.50
ACGTcount: A:0.46, C:0.02, G:0.08, T:0.44
Consensus pattern (10 bp):
TTAATTAAAG
Found at i:35659547 original size:30 final size:29
Alignment explanation
Indices: 35659511--35659699 Score: 207
Period size: 30 Copynumber: 6.3 Consensus size: 29
35659501 TGAGTAACCA
*
35659511 CAATTATAATGTTAGCTTGTGTGAGCAATT
1 CAATTATAATGTCAGCTTGTGTGAG-AATT
* * *
35659541 CAATTATAATGTCAGCTTGTTTAAGCAATC
1 CAATTATAATGTCAGCTTGTGTGAG-AATT
*
35659571 CGATTATAATGTCAGCTTGTGTGAGAATT
1 CAATTATAATGTCAGCTTGTGTGAGAATT
** *
35659600 CAATTATAATGTCAATTTGAGTGAGAAATT
1 CAATTATAATGTCAGCTTGTGTGAG-AATT
** *
35659630 TGATTATAATGTCAGCTTGTATGAGAAATT
1 CAATTATAATGTCAGCTTGTGTGAG-AATT
* * *
35659660 CGATTATAATGTAAGCTTGTGTGAGAAAT
1 CAATTATAATGTCAGCTTGTGTGAGAATT
35659689 CTAATTATAAT
1 C-AATTATAAT
35659700 TTCAACTTTT
Statistics
Matches: 134, Mismatches: 23, Indels: 4
0.83 0.14 0.02
Matches are distributed among these distances:
29 28 0.21
30 106 0.79
ACGTcount: A:0.34, C:0.10, G:0.19, T:0.38
Consensus pattern (29 bp):
CAATTATAATGTCAGCTTGTGTGAGAATT
Found at i:35659664 original size:89 final size:89
Alignment explanation
Indices: 35659511--35659707 Score: 259
Period size: 89 Copynumber: 2.2 Consensus size: 89
35659501 TGAGTAACCA
* * * * * *
35659511 CAATTATAATGTTAGCTTGTGTGAGCAATTCAATTATAATGTCAGCTTGTTTAAGCAATCCGATT
1 CAATTATAATGTCAACTTGAGTGAGAAATTCAATTATAATGTCAGCTTGTATAAGAAATCCGATT
* *
35659576 ATAATGTCAGCTTGTGTGAGAATT
66 ATAATGTAAGCTTGTGTGAGAAAT
* ** * *
35659600 CAATTATAATGTCAATTTGAGTGAGAAATTTGATTATAATGTCAGCTTGTATGAGAAATTCGATT
1 CAATTATAATGTCAACTTGAGTGAGAAATTCAATTATAATGTCAGCTTGTATAAGAAATCCGATT
35659665 ATAATGTAAGCTTGTGTGAGAAAT
66 ATAATGTAAGCTTGTGTGAGAAAT
*
35659689 CTAATTATAATTTCAACTT
1 C-AATTATAATGTCAACTT
35659708 TTGGGAGCAA
Statistics
Matches: 92, Mismatches: 15, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
89 77 0.84
90 15 0.16
ACGTcount: A:0.34, C:0.10, G:0.18, T:0.39
Consensus pattern (89 bp):
CAATTATAATGTCAACTTGAGTGAGAAATTCAATTATAATGTCAGCTTGTATAAGAAATCCGATT
ATAATGTAAGCTTGTGTGAGAAAT
Found at i:35661651 original size:19 final size:18
Alignment explanation
Indices: 35661627--35661667 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
35661617 CATAATGAGA
*
35661627 TAATACATTTTAAAACTAT
1 TAATACA-TATAAAACTAT
*
35661646 TAATACATATATAACTAT
1 TAATACATATAAAACTAT
35661664 TAAT
1 TAAT
35661668 TAGTCCAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (18 bp):
TAATACATATAAAACTAT
Found at i:35662136 original size:23 final size:20
Alignment explanation
Indices: 35662089--35662154 Score: 57
Period size: 20 Copynumber: 3.2 Consensus size: 20
35662079 TGTGATATAG
*
35662089 TATTACATAATATAATAACA
1 TATTACATAATATAATAAAA
*
35662109 TATTATATAACTATAACTAAAA
1 TATTACATAA-TATAA-TAAAA
35662131 CTATTA-ATACATAT-AT-AAA
1 -TATTACATA-ATATAATAAAA
35662150 TATTA
1 TATTA
35662155 TTTTATTATT
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
18 5 0.12
19 3 0.08
20 10 0.25
21 6 0.15
22 10 0.25
23 6 0.15
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (20 bp):
TATTACATAATATAATAAAA
Found at i:35663988 original size:25 final size:25
Alignment explanation
Indices: 35663926--35664006 Score: 74
Period size: 25 Copynumber: 3.2 Consensus size: 25
35663916 AGTAAGTTTT
* * * *
35663926 CTGAAACTATTTTTGATAGTATATC
1 CTGAAACTACTATAGATAGTATATA
* * *
35663951 CAGAAACTGCTATAGGTAGTATATA
1 CTGAAACTACTATAGATAGTATATA
*
35663976 CTGAGACTACTATAGATAG-ACTATA
1 CTGAAACTACTATAGATAGTA-TATA
35664001 CTGAAA
1 CTGAAA
35664007 ACACTTAAAA
Statistics
Matches: 43, Mismatches: 12, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
24 1 0.02
25 42 0.98
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (25 bp):
CTGAAACTACTATAGATAGTATATA
Found at i:35668855 original size:431 final size:431
Alignment explanation
Indices: 35668052--35668915 Score: 1719
Period size: 431 Copynumber: 2.0 Consensus size: 431
35668042 CGAGGCAGTT
*
35668052 GGGAGGATTCCCTGCCACTAGCAGAGTTTTCTTATAACAACAGCTACCAGTCTAGCATTTAGGTG
1 GGGAGGATTACCTGCCACTAGCAGAGTTTTCTTATAACAACAGCTACCAGTCTAGCATTTAGGTG
35668117 GCACCTTATGAGGCACACCTTCAGGTTAAACTAAGTTGGACGAGTGCCGTGTTCTGGGCCATAAA
66 GCACCTTATGAGGCACACCTTCAGGTTAAACTAAGTTGGACGAGTGCCGTGTTCTGGGCCATAAA
35668182 CTAGTTTCTGATACTGATGATAAAGTTAGATTGATTCAAGACCGATTGAAAGTGGCGTCCGATAG
131 CTAGTTTCTGATACTGATGATAAAGTTAGATTGATTCAAGACCGATTGAAAGTGGCGTCCGATAG
35668247 ACAGAAGTCTTACGTAGATTTGAAGTGTCTTGAAATTGAGTTTTCTGTGAGAGACTTCATTTTTC
196 ACAGAAGTCTTACGTAGATTTGAAGTGTCTTGAAATTGAGTTTTCTGTGAGAGACTTCATTTTTC
35668312 TTAAGGTCTCGCCATGGAAAAAGGTTCTGAGATTTAGTTGTAAGGGCAAGTTGAGCCCTAGGTTT
261 TTAAGGTCTCGCCATGGAAAAAGGTTCTGAGATTTAGTTGTAAGGGCAAGTTGAGCCCTAGGTTT
35668377 ATTGGACCCTATCGCATACTGAAACGGCTGGGACCGGTTGCCTACCAGTTAGAGCTACCTCTAGA
326 ATTGGACCCTATCGCATACTGAAACGGCTGGGACCGGTTGCCTACCAGTTAGAGCTACCTCTAGA
35668442 GTTGGACCAGATTCATGATGTTTTCCACGTGTCGATGTTAA
391 GTTGGACCAGATTCATGATGTTTTCCACGTGTCGATGTTAA
35668483 GGGAGGATTACCTGCCACTAGCAGAGTTTTCTTATAACAACAGCTACCAGTCTAGCATTTAGGTG
1 GGGAGGATTACCTGCCACTAGCAGAGTTTTCTTATAACAACAGCTACCAGTCTAGCATTTAGGTG
35668548 GCACCTTATGAGGCACACCTTCAGGTTAAACTAAGTTGGACGAGTGCCGTGTTCTGGGCCATAAA
66 GCACCTTATGAGGCACACCTTCAGGTTAAACTAAGTTGGACGAGTGCCGTGTTCTGGGCCATAAA
35668613 CTAGTTTCTGATACTGATGATAAAGTTAGATTGATTCAAGACCGATTGAAAGTGGCGTCCGATAG
131 CTAGTTTCTGATACTGATGATAAAGTTAGATTGATTCAAGACCGATTGAAAGTGGCGTCCGATAG
35668678 ACAGAAGTCTTACGTAGATTTGAAGTGTCTTGAAATTGAGTTTTCTGTGAGAGACTTCATTTTTC
196 ACAGAAGTCTTACGTAGATTTGAAGTGTCTTGAAATTGAGTTTTCTGTGAGAGACTTCATTTTTC
35668743 TTAAGGTCTCGCCATGGAAAAAGGTTCTGAGATTTAGTTGTAAGGGCAAGTTGAGCCCTAGGTTT
261 TTAAGGTCTCGCCATGGAAAAAGGTTCTGAGATTTAGTTGTAAGGGCAAGTTGAGCCCTAGGTTT
35668808 ATTGGACCCTATCGCATACTGAAACGGCTGGGACCGGTTGCCTACCAGTTAGAGCTACCTCTAGA
326 ATTGGACCCTATCGCATACTGAAACGGCTGGGACCGGTTGCCTACCAGTTAGAGCTACCTCTAGA
35668873 GTTGGACCAGATTCATGATGTTTTCCACGTGTCGATGTTAA
391 GTTGGACCAGATTCATGATGTTTTCCACGTGTCGATGTTAA
35668914 GG
1 GG
35668916 CGCTACCGCT
Statistics
Matches: 432, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
431 432 1.00
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.30
Consensus pattern (431 bp):
GGGAGGATTACCTGCCACTAGCAGAGTTTTCTTATAACAACAGCTACCAGTCTAGCATTTAGGTG
GCACCTTATGAGGCACACCTTCAGGTTAAACTAAGTTGGACGAGTGCCGTGTTCTGGGCCATAAA
CTAGTTTCTGATACTGATGATAAAGTTAGATTGATTCAAGACCGATTGAAAGTGGCGTCCGATAG
ACAGAAGTCTTACGTAGATTTGAAGTGTCTTGAAATTGAGTTTTCTGTGAGAGACTTCATTTTTC
TTAAGGTCTCGCCATGGAAAAAGGTTCTGAGATTTAGTTGTAAGGGCAAGTTGAGCCCTAGGTTT
ATTGGACCCTATCGCATACTGAAACGGCTGGGACCGGTTGCCTACCAGTTAGAGCTACCTCTAGA
GTTGGACCAGATTCATGATGTTTTCCACGTGTCGATGTTAA
Found at i:35675628 original size:6 final size:6
Alignment explanation
Indices: 35675619--35675668 Score: 50
Period size: 6 Copynumber: 8.7 Consensus size: 6
35675609 TTTAATCACT
* * * *
35675619 TTAATA TTAATT TTAAT- CTAATA TTAATA TT-AGA TTAAAA TTAATA
1 TTAATA TTAATA TTAATA TTAATA TTAATA TTAATA TTAATA TTAATA
35675665 TTAA
1 TTAA
35675669 AGTGATTAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
5 8 0.22
6 28 0.78
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (6 bp):
TTAATA
Found at i:35675633 original size:21 final size:23
Alignment explanation
Indices: 35675603--35675685 Score: 73
Period size: 23 Copynumber: 3.6 Consensus size: 23
35675593 TTCAACTATG
*
35675603 ATTAAATTTAATC-ACT-TTAAT
1 ATTAAATTTAATCTAATATTAAT
*
35675624 ATTAATTTTAATCTAATATTAAT
1 ATTAAATTTAATCTAATATTAAT
* *
35675647 ATTAGATTAAAAT-TAATATTAAAGT
1 ATTAAATT-TAATCTAATATT-AA-T
35675672 GATTAAATTTAATC
1 -ATTAAATTTAATC
35675686 ATAGTTGAAC
Statistics
Matches: 48, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
21 12 0.25
22 2 0.04
23 18 0.38
24 5 0.10
25 4 0.08
26 7 0.15
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.46
Consensus pattern (23 bp):
ATTAAATTTAATCTAATATTAAT
Found at i:35675642 original size:17 final size:16
Alignment explanation
Indices: 35675619--35675668 Score: 64
Period size: 17 Copynumber: 3.0 Consensus size: 16
35675609 TTTAATCACT
*
35675619 TTAATATTAATTTTAA
1 TTAATATTAATATTAA
35675635 TCTAATATTAATATTAGA
1 T-TAATATTAATATTA-A
*
35675653 TTAAAATTAATATTAA
1 TTAATATTAATATTAA
35675669 AGTGATTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
16 2 0.07
17 26 0.87
18 2 0.07
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (16 bp):
TTAATATTAATATTAA
Found at i:35685061 original size:50 final size:50
Alignment explanation
Indices: 35684987--35685178 Score: 169
Period size: 50 Copynumber: 3.8 Consensus size: 50
35684977 AAAGTGAAAG
* * *
35684987 TGAT-GGTCACGTGTGTGGTACTATGTGTAGGCTACTATGTGTACTGGAA
1 TGATAGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACTGGAA
* * * * *
35685036 TGATAGGTCGCATGTGTAGTACTATGTGTAGGGTACT-TGCGTACCGGATAA
1 TGATAGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACTGG--AA
* * * * * *
35685087 T-TTCGATCACGTGTGTAGTACTATGTGCAGGCTAGTACGTGTA-TCGG-A
1 TGATAGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACT-GGAA
*
35685135 TGGTAATGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTG
1 TGAT-A-GGTCACATGTGTAGTACTATGTGCAGGCTACTATGTG
35685179 AACCGAACAT
Statistics
Matches: 112, Mismatches: 23, Indels: 14
0.75 0.15 0.09
Matches are distributed among these distances:
48 2 0.02
49 13 0.12
50 55 0.49
51 42 0.38
ACGTcount: A:0.22, C:0.14, G:0.31, T:0.33
Consensus pattern (50 bp):
TGATAGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACTGGAA
Found at i:35685111 original size:100 final size:101
Alignment explanation
Indices: 35684993--35685173 Score: 251
Period size: 100 Copynumber: 1.8 Consensus size: 101
35684983 AAAGTGATGG
* * * *
35684993 TCACGTGTGTGGTACTATGTGTAGGCTACTATGTGTA-CTGGAATGAT-A-GGTCGCATGTGTAG
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATC-GG-ATGATAATGGTCACATGTGTAG
* *
35685055 TACTATGTGTAGGGTACTTGCGTACCGGATAATTTCGA
64 TACTATGTGCAGGCTACTTGCGTACCGGATAATTTCGA
* *
35685093 TCACGTGTGTAGTACTATGTGCAGGCTAGTACGTGTATCGGATGGTAATGGTCACATGTGTAGTA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGATAATGGTCACATGTGTAGTA
35685158 CTATGTGCAGGCTACT
66 CTATGTGCAGGCTACT
35685174 ATGTGAACCG
Statistics
Matches: 70, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
99 4 0.06
100 36 0.51
101 30 0.43
ACGTcount: A:0.22, C:0.15, G:0.30, T:0.33
Consensus pattern (101 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGATAATGGTCACATGTGTAGTA
CTATGTGCAGGCTACTTGCGTACCGGATAATTTCGA
Found at i:35685299 original size:23 final size:22
Alignment explanation
Indices: 35685273--35685316 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
35685263 AATTGACTAA
35685273 GTGT-AATTGAATAATGAATATAG
1 GTGTGAATTGAAT--TGAATATAG
35685296 GTGTGGAATTGAATTGAATAT
1 GTGT-GAATTGAATTGAATAT
35685317 CGACTTAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.39, C:0.00, G:0.25, T:0.36
Consensus pattern (22 bp):
GTGTGAATTGAATTGAATATAG
Found at i:35689530 original size:17 final size:18
Alignment explanation
Indices: 35689503--35689537 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
35689493 GTGAATGGGT
35689503 TTTTTTAATTATATTTTA
1 TTTTTTAATTATATTTTA
*
35689521 TTTTTT-ATTATCTTTTA
1 TTTTTTAATTATATTTTA
35689538 ATTATGAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTTTTAATTATATTTTA
Done.