Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008124.1 Hibiscus syriacus cultivar Beakdansim tig00110678_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3296903
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 19
Found at i:1393107 original size:139 final size:139
Alignment explanation
Indices: 1392841--1393149 Score: 370
Period size: 139 Copynumber: 2.2 Consensus size: 139
1392831 TAATTTTCAA
** *
1392841 ATTAACCGAACCGAATTAACCGAATTTTTTGCTTCGATTAATTCAGTTAATAGTTTTCAAAAAAT
1 ATTAACCGAACAAAATTAACCGAA-TTTTTGCTTCAATTAATTCAGTTAATAGTTTTCAAAAAAT
* ** * * * *
1392906 ATCGGTTAATTTTGTTCGTTTATAATTTTCAAATTAATTTGGTTCGGTTAATAATTTTAAATAAA
65 ATCGATTAATTCAGTTCGTTAATAATTTTCAAATTAATTCGATTCGGTTAATAATTTCAAATAAA
*
1392971 TTTTGGTTCG
130 GTTTGGTTCG
* * ****
1392981 ATTAATCGAACAAAATTAACCGAATTTTTGCTTCAATTAATTCGGTTAATA-TTTTTTTTAAAT-
1 ATTAACCGAACAAAATTAACCGAATTTTTGCTTCAATTAATTCAGTTAATAGTTTTCAAAAAATA
* *
1393044 TCGATTAATTCAGTTCGATTAATAATTTTTAAATTAATTCGATTTGGTTAATAATATTCAAATAA
66 TCGATTAATTCAGTTCG-TTAATAATTTTCAAATTAATTCGATTCGGTTAATAAT-TTCAAATAA
1393109 AGTTTGGTTCG
129 AGTTTGGTTCG
** *
1393120 ATTAACCGAACTGAATTAATCGAAATTTTT
1 ATTAACCGAACAAAATTAACCG-AATTTTT
1393150 TCTTTAACCG
Statistics
Matches: 143, Mismatches: 23, Indels: 6
0.83 0.13 0.03
Matches are distributed among these distances:
137 14 0.10
138 40 0.28
139 61 0.43
140 28 0.20
ACGTcount: A:0.34, C:0.10, G:0.12, T:0.44
Consensus pattern (139 bp):
ATTAACCGAACAAAATTAACCGAATTTTTGCTTCAATTAATTCAGTTAATAGTTTTCAAAAAATA
TCGATTAATTCAGTTCGTTAATAATTTTCAAATTAATTCGATTCGGTTAATAATTTCAAATAAAG
TTTGGTTCG
Found at i:1394489 original size:21 final size:21
Alignment explanation
Indices: 1394460--1394580 Score: 133
Period size: 20 Copynumber: 5.8 Consensus size: 21
1394450 AGATTGTCCA
1394460 GGGGTACAGATTCCCCCTCAG
1 GGGGTACAGATTCCCCCTCAG
*
1394481 GGGGAACAGATTCCCCC-CAG
1 GGGGTACAGATTCCCCCTCAG
*
1394501 GGGGTACCGATTCCCCCT-AG
1 GGGGTACAGATTCCCCCTCAG
* *
1394521 GGGGTACCGATTCCCCTTCA-
1 GGGGTACAGATTCCCCCTCAG
*
1394541 GGGGTAACAGATTCCCCC-CATAA
1 GGGGT-ACAGATTCCCCCTC--AG
*
1394564 GGGGTACCGATTCCCCC
1 GGGGTACAGATTCCCCC
1394581 ATGTCTAACG
Statistics
Matches: 87, Mismatches: 7, Indels: 11
0.83 0.07 0.10
Matches are distributed among these distances:
20 43 0.49
21 27 0.31
22 12 0.14
23 5 0.06
ACGTcount: A:0.20, C:0.35, G:0.27, T:0.18
Consensus pattern (21 bp):
GGGGTACAGATTCCCCCTCAG
Found at i:1394507 original size:41 final size:40
Alignment explanation
Indices: 1394456--1394558 Score: 136
Period size: 41 Copynumber: 2.5 Consensus size: 40
1394446 AATCAGATTG
1394456 TCCAGGGGTACAGATTCCCCCTCAGGGGGAACAGATTCCCC
1 TCCAGGGGTACAGATTCCCCCT-AGGGGGAACAGATTCCCC
* * *
1394497 -CCAGGGGGTACCGATTCCCCCTAGGGGGTACCGATTCCCC
1 TCCA-GGGGTACAGATTCCCCCTAGGGGGAACAGATTCCCC
*
1394537 TTCAGGGGTAACAGATTCCCCC
1 TCCAGGGGT-ACAGATTCCCCC
1394559 CATAAGGGGT
Statistics
Matches: 54, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
40 24 0.44
41 30 0.56
ACGTcount: A:0.19, C:0.35, G:0.27, T:0.18
Consensus pattern (40 bp):
TCCAGGGGTACAGATTCCCCCTAGGGGGAACAGATTCCCC
Found at i:1394553 original size:61 final size:62
Alignment explanation
Indices: 1394460--1394580 Score: 190
Period size: 61 Copynumber: 2.0 Consensus size: 62
1394450 AGATTGTCCA
*
1394460 GGGGTACAGATTCCCCCTCAGGGGGAACAGATTCCCCCC-AGGGGGTACCGATTCCCCCTAG
1 GGGGTACAGATTCCCCCTCAGGGGGAACAGATTCCCCCCAAAGGGGTACCGATTCCCCCTAG
* * *
1394521 GGGGTACCGATTCCCCTTCAGGGGTAACAGATTCCCCCCATAAGGGGTACCGATTCCCCC
1 GGGGTACAGATTCCCCCTCAGGGGGAACAGATTCCCCCCA-AAGGGGTACCGATTCCCCC
1394581 ATGTCTAACG
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
61 36 0.67
63 18 0.33
ACGTcount: A:0.20, C:0.35, G:0.27, T:0.18
Consensus pattern (62 bp):
GGGGTACAGATTCCCCCTCAGGGGGAACAGATTCCCCCCAAAGGGGTACCGATTCCCCCTAG
Found at i:1398010 original size:20 final size:21
Alignment explanation
Indices: 1397963--1398043 Score: 78
Period size: 20 Copynumber: 4.0 Consensus size: 21
1397953 ATCAGATTGT
* *
1397963 CCAGGGGGTACAGATT-ACCC
1 CCAGGGGGTACCGATTCCCCC
*
1397983 TCAGGGGGTACCGATTCCCCC
1 CCAGGGGGTACCGATTCCCCC
* **
1398004 CCA-GGGGAACAAATT-CCCC
1 CCAGGGGGTACCGATTCCCCC
*
1398023 CTAGGGGGTACCGATTCCCCC
1 CCAGGGGGTACCGATTCCCCC
1398044 TGTCTAACGG
Statistics
Matches: 47, Mismatches: 11, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
19 6 0.13
20 32 0.68
21 9 0.19
ACGTcount: A:0.21, C:0.36, G:0.27, T:0.16
Consensus pattern (21 bp):
CCAGGGGGTACCGATTCCCCC
Found at i:1406429 original size:32 final size:31
Alignment explanation
Indices: 1406388--1406511 Score: 94
Period size: 31 Copynumber: 4.0 Consensus size: 31
1406378 AGTCGAGGGT
1406388 TTACCTATGTTCTACGGAACATATGGACAGAA
1 TTACCTATGTTCTACGGAACATATGGACAG-A
* *
1406420 TTACCTATG-TCTTTC-GAGACATATAGACAG-
1 TTACCTATGTTC-TACGGA-ACATATGGACAGA
* * * *
1406450 TATATCTATATTCTAAGGAACATATGGACAGT
1 T-TACCTATGTTCTACGGAACATATGGACAGA
* * *
1406482 TTACCTAGGTTCTTCGGGATC-TATGGACAG
1 TTACCTATGTTCTAC-GGAACATATGGACAG
1406512 TTGTCGAGGT
Statistics
Matches: 72, Mismatches: 13, Indels: 15
0.72 0.13 0.15
Matches are distributed among these distances:
30 1 0.01
31 40 0.56
32 31 0.43
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Consensus pattern (31 bp):
TTACCTATGTTCTACGGAACATATGGACAGA
Found at i:1407601 original size:22 final size:22
Alignment explanation
Indices: 1407576--1407621 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
1407566 TATGTTGTCT
1407576 TGCTAATAGAATAAGATTTGTA
1 TGCTAATAGAATAAGATTTGTA
1407598 TGCTAATAGAATAAGATTTGTA
1 TGCTAATAGAATAAGATTTGTA
1407620 TG
1 TG
1407622 ATATAGTAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.39, C:0.04, G:0.20, T:0.37
Consensus pattern (22 bp):
TGCTAATAGAATAAGATTTGTA
Found at i:1410302 original size:25 final size:25
Alignment explanation
Indices: 1410274--1410335 Score: 67
Period size: 25 Copynumber: 2.5 Consensus size: 25
1410264 ACACTTGTGA
1410274 TATATGTG-ATAT-TAATATAAGTAAT
1 TATATG-GAATATGTAATATAAGT-AT
*
1410299 TATA-GGAATATGTAATATAAGTGT
1 TATATGGAATATGTAATATAAGTAT
*
1410323 TATATGAAATATG
1 TATATGGAATATG
1410336 ACTATGTGAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
23 1 0.03
24 10 0.31
25 21 0.66
ACGTcount: A:0.44, C:0.00, G:0.16, T:0.40
Consensus pattern (25 bp):
TATATGGAATATGTAATATAAGTAT
Found at i:1410745 original size:31 final size:31
Alignment explanation
Indices: 1410661--1410784 Score: 142
Period size: 31 Copynumber: 4.0 Consensus size: 31
1410651 GTCGAGGGTT
* * *
1410661 TACCTATGTTCTACGGAACATATGGACAGAA
1 TACCTATGTTCTAAGGAACATAGGGACAGTA
*** *
1410692 TTACCTATG-TCTTTCGAGACATATGGACAGTA
1 -TACCTATGTTCTAAGGA-ACATAGGGACAGTA
* *
1410724 TACCTATGTTCTAAGGAACATAGGGATAATA
1 TACCTATGTTCTAAGGAACATAGGGACAGTA
1410755 TACCTATGTTCTAAGGAACATAGGGACAGT
1 TACCTATGTTCTAAGGAACATAGGGACAGT
1410785 TTACTTAGGT
Statistics
Matches: 78, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
31 52 0.67
32 26 0.33
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (31 bp):
TACCTATGTTCTAAGGAACATAGGGACAGTA
Found at i:1412479 original size:94 final size:94
Alignment explanation
Indices: 1412318--1412489 Score: 317
Period size: 94 Copynumber: 1.8 Consensus size: 94
1412308 AGAGTCAAGA
1412318 CTTTTCGGTTTACCATATCTTTACAAAAAATATTTCAAATTAATTGTTCCACTTTTTATTGATAG
1 CTTTTCGGTTTACCATATCTTTACAAAAAATATTTCAAATTAATTGTTCCACTTTTTATTGATAG
*
1412383 GTTATACACAGTCCATACGTCCTTAAACC
66 GTTACACACAGTCCATACGTCCTTAAACC
* *
1412412 CTTTTCGGTTTATCATATCTTTACAAAAATTATTTCAAATTAATTGTTCCACTTTTTATTGATAG
1 CTTTTCGGTTTACCATATCTTTACAAAAAATATTTCAAATTAATTGTTCCACTTTTTATTGATAG
1412477 GTTACACACAGTC
66 GTTACACACAGTC
1412490 TATATGTGAG
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
94 75 1.00
ACGTcount: A:0.30, C:0.19, G:0.09, T:0.42
Consensus pattern (94 bp):
CTTTTCGGTTTACCATATCTTTACAAAAAATATTTCAAATTAATTGTTCCACTTTTTATTGATAG
GTTACACACAGTCCATACGTCCTTAAACC
Found at i:1414492 original size:18 final size:19
Alignment explanation
Indices: 1414465--1414502 Score: 69
Period size: 18 Copynumber: 2.1 Consensus size: 19
1414455 GTAAGTAAAA
1414465 AAAAACCTTCAATATATAT
1 AAAAACCTTCAATATATAT
1414484 AAAAA-CTTCAATATATAT
1 AAAAACCTTCAATATATAT
1414502 A
1 A
1414503 TATATATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (19 bp):
AAAAACCTTCAATATATAT
Found at i:1414499 original size:2 final size:2
Alignment explanation
Indices: 1414494--1414520 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1414484 AAAAACTTCA
1414494 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1414521 CTTAAAAGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1422514 original size:21 final size:21
Alignment explanation
Indices: 1422467--1422514 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
1422457 CCTTCAAAAT
1422467 TTAAAATTATCATATATTATA
1 TTAAAATTATCATATATTATA
** *
1422488 AAAAAATTTAT-ATATATTTTA
1 TTAAAA-TTATCATATATTATA
1422509 TTAAAA
1 TTAAAA
1422515 ATATAATTTT
Statistics
Matches: 21, Mismatches: 5, Indels: 2
0.75 0.18 0.07
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (21 bp):
TTAAAATTATCATATATTATA
Found at i:1422590 original size:29 final size:28
Alignment explanation
Indices: 1422535--1422590 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
1422525 ACACTAATAT
*
1422535 ATTTTATAAATTTAATTCAATTTTTAAA
1 ATTTTATAAATTTAATTCAATCTTTAAA
1422563 ATTTTATAAATTTAAATTC-ATCCTTTAA
1 ATTTTATAAATTT-AATTCAAT-CTTTAA
1422591 TATATCATCT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 15 0.60
29 10 0.40
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (28 bp):
ATTTTATAAATTTAATTCAATCTTTAAA
Found at i:1424130 original size:17 final size:16
Alignment explanation
Indices: 1424108--1424152 Score: 58
Period size: 17 Copynumber: 2.9 Consensus size: 16
1424098 CGCATCAAAA
1424108 TTTTAAAAAATATATAT
1 TTTTAAAAAATATAT-T
*
1424125 TTTTAAATAATAT-TT
1 TTTTAAAAAATATATT
1424140 TTTT-AAAAATATA
1 TTTTAAAAAATATA
1424153 AACGTAACAC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
14 7 0.28
15 5 0.20
16 1 0.04
17 12 0.48
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TTTTAAAAAATATATT
Found at i:1424141 original size:14 final size:15
Alignment explanation
Indices: 1424115--1424152 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
1424105 AAATTTTAAA
1424115 AAAT-ATATATTTTT
1 AAATAATATATTTTT
*
1424129 AAATAATATTTTTTT
1 AAATAATATATTTTT
1424144 AAA-AATATA
1 AAATAATATA
1424153 AACGTAACAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 9 0.43
15 12 0.57
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
AAATAATATATTTTT
Found at i:1426525 original size:20 final size:20
Alignment explanation
Indices: 1426500--1426542 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1426490 TCTAAGAGCC
*
1426500 CATTTAGGACCATTTAGATG
1 CATTTAGGACCATATAGATG
* *
1426520 CATTTAGGAGCATATAGTTG
1 CATTTAGGACCATATAGATG
1426540 CAT
1 CAT
1426543 GTGGTGGATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35
Consensus pattern (20 bp):
CATTTAGGACCATATAGATG
Found at i:1434220 original size:13 final size:13
Alignment explanation
Indices: 1434199--1434233 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
1434189 CCCACTTACT
1434199 TTTCACTTTTCAC
1 TTTCACTTTTCAC
* *
1434212 TTTCTCTTTTTAC
1 TTTCACTTTTCAC
1434225 TTTCACTTT
1 TTTCACTTT
1434234 CTAGTTTCCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.11, C:0.26, G:0.00, T:0.63
Consensus pattern (13 bp):
TTTCACTTTTCAC
Found at i:1439398 original size:250 final size:241
Alignment explanation
Indices: 1438879--1439473 Score: 685
Period size: 254 Copynumber: 2.4 Consensus size: 241
1438869 TTCATATATC
*
1438879 GAATAAAAATATTTTTTATTATTTCAGGTTGGGTCGGGTTTCTAATTCATATATTCGGGTCGGGT
1 GAATAAAAATA-TTTTTATTATTTC-GGTCGGGTC-GGTTTCTAATTCATATA----GGTCGGGT
* *
1438944 CGGGTGAAACTTT-GTTT--T--GGTCGGGTAAGTTTTTTAAGTGTGATATTCGGGTTGGGTCGA
59 CGGGTGAAACTTTATTTTGGTCAGGTCGGGT-CGTTTTTTAAGTGTGATATTC--G--GGGTCGA
1439004 GTTCGGGTTTAGGGTGAAAAATACCCGACCCAAAAATATATATAATTTTACCTTATATATTTAGG
119 GTTCGGGTTTAGGGTGAAAAATACCCGACCCAAAAATATATATAATTTTACCTTATATATTTAGG
* *
1439069 AATAATTACAATAATTCCCTCTATATATAATTTTTTCAATTAAGTCACTTTTTTTATT
184 AATAATTACAATAATACCCTCTATATATAATTTTTTCAATTAAGTCACTGTTTTTATT
1439127 GAATAAAAATAATTTTTTTATTATTTCGGGTCGGGTCGGATTTCTAATTCATATA-GTCGGGTCG
1 GAATAAAAAT-A--TTTTTATTATTTC-GGTCGGGTCGG-TTTCTAATTCATATAGGTCGGGTCG
*
1439191 GGTGAAACTTTATTTTGGTCAGGTCGGGTCGTTTTTTTAAGTGTGATATTC-GGGTCGGGTTCGG
61 GGTGAAACTTTATTTTGGTCAGGTCGGGTCG-TTTTTTAAGTGTGATATTCGGGGTCGAGTTCGG
1439255 GTTTAGGGTGAAAAATACCTGACCCAACCTGACCCAAAAA-ATATATAATTTTACCTTATATATT
125 GTTTAGGGTG-AAAA-A--T-A--C--CC-GACCCAAAAATATATATAATTTTACCTTATATATT
*
1439319 TATGAATAATTACAATAATACCC-CTATATAT-ATTTTTTCCCAATTAAGTCACTGTTTTTATT
180 TAGGAATAATTACAATAATACCCTCTATATATAATTTTTT--CAATTAAGTCACTGTTTTTATT
* *
1439381 GAATAAAAATA-TTTTATTATTAT--TTCGGGTCAGGTTTCTAATTCATATATTCGGGTCAGGTC
1 GAATAAAAATATTTTTATTATT-TCGGTCGGGTC-GGTTTCTAATTCATATA----GGTCGGGTC
*
1439443 GGGTGAAACTTTATTTTGGTCAGGTCAGGTC
60 GGGTGAAACTTTATTTTGGTCAGGTCGGGTC
1439474 TCGGATGGAG
Statistics
Matches: 308, Mismatches: 11, Indels: 51
0.83 0.03 0.14
Matches are distributed among these distances:
245 42 0.14
246 7 0.02
247 1 0.00
248 33 0.11
249 7 0.02
250 75 0.24
251 1 0.00
252 8 0.03
253 46 0.15
254 78 0.25
255 10 0.03
ACGTcount: A:0.28, C:0.13, G:0.19, T:0.40
Consensus pattern (241 bp):
GAATAAAAATATTTTTATTATTTCGGTCGGGTCGGTTTCTAATTCATATAGGTCGGGTCGGGTGA
AACTTTATTTTGGTCAGGTCGGGTCGTTTTTTAAGTGTGATATTCGGGGTCGAGTTCGGGTTTAG
GGTGAAAAATACCCGACCCAAAAATATATATAATTTTACCTTATATATTTAGGAATAATTACAAT
AATACCCTCTATATATAATTTTTTCAATTAAGTCACTGTTTTTATT
Found at i:1439865 original size:17 final size:17
Alignment explanation
Indices: 1439830--1439874 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
1439820 ATGGAATTGA
* * *
1439830 ATTCCAATTCCTGATAG
1 ATTCCAATTCTTCACAG
1439847 ATTCCAATTCTTCACAG
1 ATTCCAATTCTTCACAG
*
1439864 ATTACAATTCT
1 ATTCCAATTCT
1439875 CTCATAAACA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.31, C:0.24, G:0.07, T:0.38
Consensus pattern (17 bp):
ATTCCAATTCTTCACAG
Found at i:1445111 original size:3 final size:3
Alignment explanation
Indices: 1445103--1445128 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1445093 CCTACAGTAA
1445103 GCT GCT GCT GCT GCT GCT GCT GCT GC
1 GCT GCT GCT GCT GCT GCT GCT GCT GC
1445129 AACTGATTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.35, T:0.31
Consensus pattern (3 bp):
GCT
Found at i:1445147 original size:51 final size:51
Alignment explanation
Indices: 1445059--1445158 Score: 146
Period size: 51 Copynumber: 2.0 Consensus size: 51
1445049 CAACAATATT
* * *
1445059 CTGCTGCTGCTGCTGCTGCAAATGACTAGGGATTCCTACAGTAAGCTGCTG
1 CTGCTGCTGCTGCTGCTGCAAATGACTAGAGACTCCTACACTAAGCTGCTG
* * *
1445110 CTGCTGCTGCTGCTGCTGCAACTGATTAGAGACTCCTACACTAGGCTGC
1 CTGCTGCTGCTGCTGCTGCAAATGACTAGAGACTCCTACACTAAGCTGC
1445159 GGTTGGTGGT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 43 1.00
ACGTcount: A:0.19, C:0.28, G:0.26, T:0.27
Consensus pattern (51 bp):
CTGCTGCTGCTGCTGCTGCAAATGACTAGAGACTCCTACACTAAGCTGCTG
Found at i:1449764 original size:28 final size:28
Alignment explanation
Indices: 1449724--1449779 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
1449714 AAATTGACAT
1449724 TAAAATCATAGGTAAACATTTATAATTG
1 TAAAATCATAGGTAAACATTTATAATTG
*
1449752 TAAAATCATAGGTAAACATTTATCATTG
1 TAAAATCATAGGTAAACATTTATAATTG
1449780 GAATGATCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.45, C:0.09, G:0.11, T:0.36
Consensus pattern (28 bp):
TAAAATCATAGGTAAACATTTATAATTG
Found at i:1449869 original size:60 final size:60
Alignment explanation
Indices: 1449797--1449914 Score: 168
Period size: 60 Copynumber: 2.0 Consensus size: 60
1449787 CAAACTATGG
1449797 TTCTCATTCTAAATCGA-TC-CTTAAACTTTTGAACATTCCAATTCCATCCCTAAATTATAA
1 TTCTCATTCTAAAT-GAGTCGC-TAAACTTTTGAACATTCCAATTCCATCCCTAAATTATAA
* * * *
1449857 TTCTCATTCTAAATTAGTCGCTAAAGTTTTGAGCATTCCAATTCCATCCCTACATTAT
1 TTCTCATTCTAAATGAGTCGCTAAACTTTTGAACATTCCAATTCCATCCCTAAATTAT
1449915 GACCCTAATT
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
59 1 0.02
60 50 0.96
61 1 0.02
ACGTcount: A:0.31, C:0.25, G:0.06, T:0.39
Consensus pattern (60 bp):
TTCTCATTCTAAATGAGTCGCTAAACTTTTGAACATTCCAATTCCATCCCTAAATTATAA
Found at i:1449926 original size:60 final size:60
Alignment explanation
Indices: 1449818--1449949 Score: 165
Period size: 60 Copynumber: 2.2 Consensus size: 60
1449808 AATCGATCCT
** *
1449818 TAAACTTTTGAACATTCCAATTCCATCCCTAAATTATAATTCTCATTCTAAATTAGTCGC
1 TAAACTTTTGAACATTCCAATTCCATCCCTAAATTATAACCCTAATTCTAAATTAGTCGC
* * * * * *
1449878 TAAAGTTTTGAGCATTCCAATTCCATCCCTACATTATGACCCTAATTCTATATTAGTCCC
1 TAAACTTTTGAACATTCCAATTCCATCCCTAAATTATAACCCTAATTCTAAATTAGTCGC
* *
1449938 CAAACTATTGAA
1 TAAACTTTTGAA
1449950 TGTTTTAGTT
Statistics
Matches: 59, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
60 59 1.00
ACGTcount: A:0.33, C:0.24, G:0.07, T:0.36
Consensus pattern (60 bp):
TAAACTTTTGAACATTCCAATTCCATCCCTAAATTATAACCCTAATTCTAAATTAGTCGC
Found at i:1453986 original size:3 final size:3
Alignment explanation
Indices: 1453978--1454076 Score: 67
Period size: 3 Copynumber: 33.3 Consensus size: 3
1453968 TTTTACTTAA
* ** * *
1453978 ATT ATT ATT TTT AAA ATT ATT ATT ATT ATT ATT AAAT ATT AGT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT
* * * * * * *
1454024 A-T AAT AAT AAT AAT AAT ATT ATT ATT ATT ATA AAT ATT ATT A-T ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1454070 ATT ATT A
1 ATT ATT A
1454077 ATAAATAATT
Statistics
Matches: 78, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
2 4 0.05
3 72 0.92
4 2 0.03
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (3 bp):
ATT
Found at i:1454978 original size:21 final size:21
Alignment explanation
Indices: 1454952--1455004 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
1454942 GTTTCCAAAT
1454952 TCGCAACGCGAACTTCGACTA
1 TCGCAACGCGAACTTCGACTA
*
1454973 TCGCAACGCGAACTTGGACTA
1 TCGCAACGCGAACTTCGACTA
*
1454994 TCGCAATGCGA
1 TCGCAACGCGA
1455005 TTTACATATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.28, C:0.30, G:0.23, T:0.19
Consensus pattern (21 bp):
TCGCAACGCGAACTTCGACTA
Found at i:1455039 original size:21 final size:20
Alignment explanation
Indices: 1455012--1455326 Score: 194
Period size: 21 Copynumber: 15.3 Consensus size: 20
1455002 CGATTTACAT
1455012 ATTCGCATTGCGATAGTCCAA
1 ATTCGC-TTGCGATAGTCCAA
* *
1455033 GTTCGCATTGCGATAGTCGAA
1 ATTCGC-TTGCGATAGTCCAA
* * **
1455054 GTTCGCGTTGCAATTTTCCAA
1 ATTCGC-TTGCGATAGTCCAA
* *
1455075 ATTTG-TTGCGATAGTCGAA
1 ATTCGCTTGCGATAGTCCAA
* **
1455094 GTTCGCGTTGCGATTTTCCAA
1 ATTCGC-TTGCGATAGTCCAA
*
1455115 ATTCG-TTGCGATAGTCGAA
1 ATTCGCTTGCGATAGTCCAA
* **
1455134 GTTCGCGTTGCGATTTTCCAA
1 ATTCGC-TTGCGATAGTCCAA
*
1455155 ATTCG-TTGCGATAGTCGAA
1 ATTCGCTTGCGATAGTCCAA
* *
1455174 GTTCGCGTTGCGATTTATTCCAA
1 ATTCGC-TTGCGA--TAGTCCAA
* *
1455197 ATTCG-TTGCGATGTATTCTAA
1 ATTCGCTTGCGA--TAGTCCAA
*
1455218 ATTCG-TTGCGATAGTCGAA
1 ATTCGCTTGCGATAGTCCAA
* **
1455237 GTTCGCGTTGCGATTTTTTCCAA
1 ATTCGC-TTGCGA--TAGTCCAA
1455260 ATTCG-TTGCGATAGTCCAA
1 ATTCGCTTGCGATAGTCCAA
* *
1455279 GTTCGCGTTGCGATTTATTCCAA
1 ATTCGC-TTGCGA--TAGTCCAA
1455302 ATTCG-TTGCGATAGTCCAA
1 ATTCGCTTGCGATAGTCCAA
*
1455321 AATCGC
1 ATTCGC
1455327 AACGACCGGT
Statistics
Matches: 227, Mismatches: 50, Indels: 35
0.73 0.16 0.11
Matches are distributed among these distances:
19 74 0.33
21 123 0.54
23 30 0.13
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.35
Consensus pattern (20 bp):
ATTCGCTTGCGATAGTCCAA
Found at i:1455089 original size:40 final size:40
Alignment explanation
Indices: 1455040--1455208 Score: 284
Period size: 40 Copynumber: 4.2 Consensus size: 40
1455030 CAAGTTCGCA
*
1455040 TTGCGATAGTCGAAGTTCGCGTTGCAATTTTCCAAATTTG
1 TTGCGATAGTCGAAGTTCGCGTTGCAATTTTCCAAATTCG
*
1455080 TTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCAATTTTCCAAATTCG
*
1455120 TTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCAATTTTCCAAATTCG
*
1455160 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGC-AATT-TTCCAAATTCG
1455202 TTGCGAT
1 TTGCGAT
1455209 GTATTCTAAA
Statistics
Matches: 123, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
40 103 0.84
41 2 0.02
42 18 0.15
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.36
Consensus pattern (40 bp):
TTGCGATAGTCGAAGTTCGCGTTGCAATTTTCCAAATTCG
Found at i:1455136 original size:80 final size:80
Alignment explanation
Indices: 1455013--1455208 Score: 302
Period size: 80 Copynumber: 2.4 Consensus size: 80
1455003 GATTTACATA
* ** *
1455013 TTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCGAAGTTCGCGTTGCAATTTTCCAAATT
1 TTCGCGTTGCGATTTTCCAAATTCG--TTGCGATAGTCGAAGTTCGCGTTGCAATTTTCCAAATT
*
1455078 TGTTGCGATAGTCGAAG
64 CGTTGCGATAGTCGAAG
*
1455095 TTCGCGTTGCGATTTTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCG
1 TTCGCGTTGCGATTTTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCAATTTTCCAAATTCG
1455160 TTGCGATAGTCGAAG
66 TTGCGATAGTCGAAG
1455175 TTCGCGTTGCGATTTATTCCAAATTCGTTGCGAT
1 TTCGCGTTGCGA-TT-TTCCAAATTCGTTGCGAT
1455209 GTATTCTAAA
Statistics
Matches: 106, Mismatches: 6, Indels: 4
0.91 0.05 0.03
Matches are distributed among these distances:
80 65 0.61
81 2 0.02
82 39 0.37
ACGTcount: A:0.21, C:0.20, G:0.24, T:0.35
Consensus pattern (80 bp):
TTCGCGTTGCGATTTTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCAATTTTCCAAATTCG
TTGCGATAGTCGAAG
Found at i:1455233 original size:63 final size:61
Alignment explanation
Indices: 1455040--1455271 Score: 233
Period size: 63 Copynumber: 3.8 Consensus size: 61
1455030 CAAGTTCGCA
* * ** * *
1455040 TTGCGATAGTCGAAGTTCGCGTTGC-AATT-TTCCAAATTTGTTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATTTTCCAAATT--CG
** * * * * *
1455101 TTGCGATTTTCCAAATT--CGTTGCGA--TAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT--CGTTGCGATTTTCCAAATTCG
*
1455160 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATGTATTCTAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGAT-T-TTCCAAATTCG
*
1455223 TTGCGATAGTCGAAGTTCGCGTTGCGATTTTTTCCAAATTCGTTGCGAT
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGAT
1455272 AGTCCAAGTT
Statistics
Matches: 140, Mismatches: 21, Indels: 18
0.78 0.12 0.10
Matches are distributed among these distances:
58 1 0.01
59 27 0.19
60 1 0.01
61 44 0.31
62 1 0.01
63 66 0.47
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.37
Consensus pattern (61 bp):
TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATTTTCCAAATTCG
Found at i:1455421 original size:6 final size:6
Alignment explanation
Indices: 1455410--1455442 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
1455400 GACACGTATT
*
1455410 ACCACG ACCACG ACCACG GCCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1455443 TGAGACAAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.30, C:0.52, G:0.18, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:1456115 original size:42 final size:42
Alignment explanation
Indices: 1456053--1456283 Score: 385
Period size: 42 Copynumber: 5.5 Consensus size: 42
1456043 TGCGATTTTG
* *
1456053 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTT
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
*
1456095 GACTATCGCAACGAACTTGGAATAAATCGCATCGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
*
1456137 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
1456179 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
*
1456221 GACTATCGCAACGAATTTGG-A-AAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
1456261 GACTATCGCAACGCGAACTTGGA
1 GACTATCGCAA--CGAACTTGGA
1456284 CTATCACAAT
Statistics
Matches: 178, Mismatches: 8, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
40 30 0.17
41 1 0.01
42 147 0.83
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.21
Consensus pattern (42 bp):
GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
Found at i:1456268 original size:21 final size:21
Alignment explanation
Indices: 1456050--1456288 Score: 201
Period size: 21 Copynumber: 11.5 Consensus size: 21
1456040 TGTTGCGATT
*
1456050 TTGGACTATCGCAA--CGAAT
1 TTGGACTATCGCAACGCGAAC
*
1456069 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAACGCGAAC
*
1456092 TTTGACTATCGCAA--CGAAC
1 TTGGACTATCGCAACGCGAAC
* *
1456111 TTGGAATAAATCGCATCGCGAAC
1 TTGGACT--ATCGCAACGCGAAC
* *
1456134 TTCGACTATCGCAA--CGAAT
1 TTGGACTATCGCAACGCGAAC
*
1456153 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAACGCGAAC
*
1456176 TTCGACTATCGCAA--CGAAC
1 TTGGACTATCGCAACGCGAAC
*
1456195 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAACGCGAAC
* *
1456218 TTCGACTATCGCAA--CGAAT
1 TTGGACTATCGCAACGCGAAC
**
1456237 TTGGAAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGCGAAC
*
1456258 TTCGACTATCGCAACGCGAAC
1 TTGGACTATCGCAACGCGAAC
1456279 TTGGACTATC
1 TTGGACTATC
1456289 ACAATGAGAA
Statistics
Matches: 173, Mismatches: 29, Indels: 34
0.73 0.12 0.14
Matches are distributed among these distances:
19 50 0.29
21 85 0.49
23 38 0.22
ACGTcount: A:0.34, C:0.25, G:0.20, T:0.22
Consensus pattern (21 bp):
TTGGACTATCGCAACGCGAAC
Found at i:1456768 original size:3 final size:3
Alignment explanation
Indices: 1456760--1456786 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1456750 AATATACTTA
1456760 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1456787 TAGTCATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1456858 original size:15 final size:16
Alignment explanation
Indices: 1456831--1456861 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
1456821 TTATCTTATT
1456831 TATAAATTTAATTTTA
1 TATAAATTTAATTTTA
1456847 TATAAA-TTAATTTTA
1 TATAAATTTAATTTTA
1456862 AGAAAAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TATAAATTTAATTTTA
Found at i:1457145 original size:142 final size:145
Alignment explanation
Indices: 1456879--1457152 Score: 346
Period size: 142 Copynumber: 1.9 Consensus size: 145
1456869 TAATCATATT
* *
1456879 TTAATACTTATTTATTTTTTAATATTAAGTAATGGGATGTATTAAAGCACCTAGAAGTCATTTTC
1 TTAATACTTATTTATTTTTTAATATTAAGAAATGGGATGTATTAAAGCACCTAGAAGTCATTTTA
* * * * * * *
1456944 TGATATTCTTAAATAAATAAATATCATTTTTTTATAAATTATATATTAATTTATTTTAAT-TATT
66 TGATATTCTTAAATAAATAAATATCATTTTTATAAAAATAAAAAATTAA-TGATATTAATATATT
1457008 TTAGAGAAATGTTTTA
130 TTAGAGAAATGTTTTA
* *
1457024 TTAATA-TTATTTA-TTTTTAATATTAAGAAAT-GGCTGTCTTAAAGCACCTAGAAGTCATTTTA
1 TTAATACTTATTTATTTTTTAATATTAAGAAATGGGATGTATTAAAGCACCTAGAAGTCATTTTA
*
1457086 TGATATT-TCTAAGTAAATAAATATC-TTATTTATAAAAATAAAAAATATACA-GATATTAATAT
66 TGATATTCT-TAAATAAATAAATATCATT-TTTATAAAAATAAAAAAT-TA-ATGATATTAATAT
1457148 ATTTT
127 ATTTT
1457153 CTTAAAATTA
Statistics
Matches: 112, Mismatches: 12, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
141 3 0.03
142 70 0.62
143 25 0.22
144 8 0.07
145 6 0.05
ACGTcount: A:0.40, C:0.06, G:0.08, T:0.46
Consensus pattern (145 bp):
TTAATACTTATTTATTTTTTAATATTAAGAAATGGGATGTATTAAAGCACCTAGAAGTCATTTTA
TGATATTCTTAAATAAATAAATATCATTTTTATAAAAATAAAAAATTAATGATATTAATATATTT
TAGAGAAATGTTTTA
Found at i:1459690 original size:6 final size:7
Alignment explanation
Indices: 1459679--1459719 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
1459669 TTTTCATACA
1459679 TGCA-TT
1 TGCATTT
1459685 TGCATTT
1 TGCATTT
*
1459692 TGTATCTT
1 TGCAT-TT
1459700 TGCATTT
1 TGCATTT
1459707 T-CATTT
1 TGCATTT
1459713 TGCATTT
1 TGCATTT
1459720 ATACTTTTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
6 10 0.33
7 14 0.47
8 6 0.20
ACGTcount: A:0.15, C:0.15, G:0.12, T:0.59
Consensus pattern (7 bp):
TGCATTT
Found at i:1459809 original size:27 final size:26
Alignment explanation
Indices: 1459779--1459834 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 26
1459769 CGTTCACATA
*
1459779 TTTACATTTGCATTTGCATTTTGCATT
1 TTTACATTTGCATTTACATTTT-CATT
* *
1459806 TTTACGTTTGTATTTACATTTTCATT
1 TTTACATTTGCATTTACATTTTCATT
1459832 TTT
1 TTT
1459835 GAATTTACAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 7 0.27
27 19 0.73
ACGTcount: A:0.18, C:0.12, G:0.09, T:0.61
Consensus pattern (26 bp):
TTTACATTTGCATTTACATTTTCATT
Found at i:1461791 original size:6 final size:7
Alignment explanation
Indices: 1461774--1461799 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
1461764 ATACATTCAA
1461774 AAAAAGG
1 AAAAAGG
1461781 AAAAAGG
1 AAAAAGG
1461788 AAAAAGG
1 AAAAAGG
1461795 AAAAA
1 AAAAA
1461800 AAGAAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (7 bp):
AAAAAGG
Found at i:1461806 original size:14 final size:14
Alignment explanation
Indices: 1461774--1461807 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
1461764 ATACATTCAA
*
1461774 AAAAAGGAAAAAGG
1 AAAAAGGAAAAAAG
1461788 AAAAAGGAAAAAAAG
1 AAAAAGG-AAAAAAG
1461803 AAAAA
1 AAAAA
1461808 TTGAATCAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.39
15 11 0.61
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (14 bp):
AAAAAGGAAAAAAG
Found at i:1467150 original size:76 final size:75
Alignment explanation
Indices: 1466934--1467409 Score: 685
Period size: 75 Copynumber: 6.4 Consensus size: 75
1466924 CTATTTCCCA
* * * *
1466934 CATCTGTAAGACCTACAGTGCATGATGTTTTC-AAAAGCCTTCGGAGTTTTTTTTATGTTTTTAA
1 CATCCGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGAG-CTTTTTGATGTTTTTAA
1466998 AGCCTCCGGGT
65 AGCCTCCGGGT
* * *
1467009 CATCCGTAAGACCTACA-TGTAGGATGTTTTCAAAAAGCCTTTGGAGCTTTTTGATTTTTTTAAA
1 CATCCGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGAGCTTTTTGATGTTTTTAAA
* *
1467073 GCCACTGGGT
66 GCCTCCGGGT
1467083 CATCCGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGTAGCTTTTTGATGTTTTTAA
1 CATCCGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGG-AGCTTTTTGATGTTTTTAA
1467148 AGCCTCCGGGT
65 AGCCTCCGGGT
*
1467159 CATCCGTAAGACCTACAGTGCAGGATGTTTT--TAAA-CCTTCGGGAGCTTTTTGATGTTTTTAA
1 CATCCGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTC-GGAGCTTTTTGATGTTTTTAA
*
1467221 AGCCTCCAGGT
65 AGCCTCCGGGT
* * *
1467232 CTTTCGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGAGAGCTTTTTGATGTTTTTAA
1 CATCCGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCG-GAGCTTTTTGATGTTTTTAA
1467297 AGCCTCCGGGT
65 AGCCTCCGGGT
* *
1467308 CATTCGTAAGACCTACA-TGCAGGATGTTTTCAAAAAGCCTTTGTGAGCTTTTTGATGTTTTTAA
1 CATCCGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCG-GAGCTTTTTGATGTTTTTAA
* *
1467372 AACCTCTGGGT
65 AGCCTCCGGGT
* *
1467383 CATCTGTAAGACCTACAGTGCAAGATG
1 CATCCGTAAGACCTACAGTGCAGGATG
1467410 ATAAGACCTC
Statistics
Matches: 362, Mismatches: 30, Indels: 17
0.89 0.07 0.04
Matches are distributed among these distances:
73 62 0.17
74 57 0.16
75 126 0.35
76 117 0.32
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (75 bp):
CATCCGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGAGCTTTTTGATGTTTTTAAA
GCCTCCGGGT
Found at i:1467240 original size:149 final size:147
Alignment explanation
Indices: 1466939--1467409 Score: 678
Period size: 149 Copynumber: 3.1 Consensus size: 147
1466929 TCCCACATCT
* *
1466939 GTAAGACCTACAGTGCATGATGTTTTC-AAAAGCCTTCGGAGTTTTTTTTATGTTTTTAAAGCCT
1 GTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGAG-CTTTTTGATGTTTTTAAAGCCT
* * *
1467003 CCGGGTCATCCGTAAGACCTACATGTAGGATGTTTTCAAAAAGCCTTTGGAGCTTTTTGATTTTT
65 CCGGGTCATCCGTAAGACCTACATGCAGGATGTTTT-AAAAAGCCTTGGGAGCTTTTTGATGTTT
* *
1467068 TTAAAGCCACTGGGTCATCC
129 TTAAAGCCTCTGGGTC-TTC
*
1467088 GTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGTAGCTTTTTGATGTTTTTAAAGCCT
1 GTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGG-AGCTTTTTGATGTTTTTAAAGCCT
*
1467153 CCGGGTCATCCGTAAGACCTACAGTGCAGGATGTTTT-TAAA-CCTTCGGGAGCTTTTTGATGTT
65 CCGGGTCATCCGTAAGACCTACA-TGCAGGATGTTTTAAAAAGCCTT-GGGAGCTTTTTGATGTT
**
1467216 TTTAAAGCCTCCAGGTCTTTC
128 TTTAAAGCCTCTGGGTC-TTC
1467237 GTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGAGAGCTTTTTGATGTTTTTAAAGCCT
1 GTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCG-GAGCTTTTTGATGTTTTTAAAGCCT
* *
1467302 CCGGGTCATTCGTAAGACCTACATGCAGGATGTTTTCAAAAAGCCTTTGTGAGCTTTTTGATGTT
65 CCGGGTCATCCGTAAGACCTACATGCAGGATGTTTT-AAAAAGCC-TTGGGAGCTTTTTGATGTT
* *
1467367 TTTAAAACCTCTGGGTCATC
128 TTTAAAGCCTCTGGGTCTTC
*
1467387 TGTAAGACCTACAGTGCAAGATG
1 -GTAAGACCTACAGTGCATGATG
1467410 ATAAGACCTC
Statistics
Matches: 291, Mismatches: 21, Indels: 18
0.88 0.06 0.05
Matches are distributed among these distances:
148 17 0.06
149 144 0.49
150 61 0.21
151 67 0.23
152 2 0.01
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (147 bp):
GTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGAGCTTTTTGATGTTTTTAAAGCCTC
CGGGTCATCCGTAAGACCTACATGCAGGATGTTTTAAAAAGCCTTGGGAGCTTTTTGATGTTTTT
AAAGCCTCTGGGTCTTC
Found at i:1467592 original size:3 final size:3
Alignment explanation
Indices: 1467584--1467648 Score: 51
Period size: 3 Copynumber: 21.3 Consensus size: 3
1467574 TTTTACATAA
* ** * *
1467584 ATT ATT ATT TTT AAA ATT ACT ATT A-T ATT ATT ATT ATT ATT AAT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
1467631 ATA ATAT ATT ATAT ATT A
1 ATT AT-T ATT AT-T ATT A
1467649 ATAATAAATA
Statistics
Matches: 47, Mismatches: 12, Indels: 6
0.72 0.18 0.09
Matches are distributed among these distances:
2 2 0.04
3 40 0.85
4 5 0.11
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.57
Consensus pattern (3 bp):
ATT
Found at i:1467612 original size:23 final size:23
Alignment explanation
Indices: 1467586--1467651 Score: 62
Period size: 23 Copynumber: 2.9 Consensus size: 23
1467576 TTACATAAAT
* *
1467586 TATTATTTTTAAAATTACTATTA
1 TATTATTATTAAAATTAATATTA
**
1467609 TATTATTATTATTATTAATATTA
1 TATTATTATTAAAATTAATATTA
* *
1467632 TAATA-TATTATATATTAATA
1 TATTATTATTA-AAATTAATA
1467652 ATAAATAATT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
22 5 0.14
23 31 0.86
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (23 bp):
TATTATTATTAAAATTAATATTA
Found at i:1467637 original size:26 final size:27
Alignment explanation
Indices: 1467584--1467654 Score: 74
Period size: 29 Copynumber: 2.6 Consensus size: 27
1467574 TTTTACATAA
* *
1467584 ATTATTATTTTTAAAATTACTATTATATT
1 ATTATTATTATTAATATTACTA-TATA-T
1467613 ATTATTATTATTAATATTA-TA-ATAT
1 ATTATTATTATTAATATTACTATATAT
*
1467638 ATTATATATTAATAATA
1 ATTAT-TATTATTAATA
1467655 AATAATTAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
25 6 0.16
26 13 0.34
28 2 0.05
29 17 0.45
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (27 bp):
ATTATTATTATTAATATTACTATATAT
Found at i:1469094 original size:57 final size:56
Alignment explanation
Indices: 1468998--1469105 Score: 132
Period size: 57 Copynumber: 1.9 Consensus size: 56
1468988 ATTTAGTCAC
1468998 TAATTTTAATACTTTCATTTATTTTACAAGCTTTATTATT-TTTATATTTTAATACTA
1 TAATTTTAATA-TTTCATTTATTTTACAAGCTTTATTATTATTTA-ATTTTAATACTA
**
1469055 TAATTTTAAT-TTTC-TTTATTTTAGTCAATTTTTAGTTATTATTTAATTTTA
1 TAATTTTAATATTTCATTTATTTTA--CAAGCTTTA-TTATTATTTAATTTTA
1469106 TATGTTTATT
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
54 9 0.20
55 4 0.09
56 7 0.16
57 21 0.47
58 4 0.09
ACGTcount: A:0.30, C:0.06, G:0.03, T:0.61
Consensus pattern (56 bp):
TAATTTTAATATTTCATTTATTTTACAAGCTTTATTATTATTTAATTTTAATACTA
Found at i:1469128 original size:15 final size:14
Alignment explanation
Indices: 1469090--1469140 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
1469080 CAATTTTTAG
1469090 TTAT-TATTTAATT
1 TTATATATTTAATT
* *
1469103 TTATATGTTTATTT
1 TTATATATTTAATT
1469117 TTAATATATTTAATT
1 TT-ATATATTTAATT
1469132 ATTAT-TATT
1 -TTATATATT
1469141 ATTATTATTA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
13 4 0.13
14 13 0.42
15 12 0.39
16 2 0.06
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (14 bp):
TTATATATTTAATT
Found at i:1469137 original size:3 final size:3
Alignment explanation
Indices: 1469129--1469158 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1469119 AATATATTTA
1469129 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1469159 TAGTCATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1472303 original size:25 final size:25
Alignment explanation
Indices: 1472269--1472320 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
1472259 CATTGGATAC
*
1472269 TAGAAATGTGTTAGCCATCTGTAAG
1 TAGAAATGTGTTAACCATCTGTAAG
1472294 TAGAAATGTGTTAACCATCTGTAAG
1 TAGAAATGTGTTAACCATCTGTAAG
1472319 TA
1 TA
1472321 CTGTTATTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.35, C:0.12, G:0.21, T:0.33
Consensus pattern (25 bp):
TAGAAATGTGTTAACCATCTGTAAG
Found at i:1476941 original size:26 final size:27
Alignment explanation
Indices: 1476887--1476952 Score: 80
Period size: 26 Copynumber: 2.4 Consensus size: 27
1476877 ATTGTATAGC
*
1476887 ATATATGATATTATATAATAATTTCAAA
1 ATATATAATA-TATATAATAATTTCAAA
* *
1476915 ATATATAATATATATAA-ATTTTGAAA
1 ATATATAATATATATAATAATTTCAAA
*
1476941 ATATATAGTATA
1 ATATATAATATA
1476953 GTTTTTGAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
26 18 0.53
27 7 0.21
28 9 0.26
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.42
Consensus pattern (27 bp):
ATATATAATATATATAATAATTTCAAA
Found at i:1476957 original size:21 final size:20
Alignment explanation
Indices: 1476921--1476963 Score: 52
Period size: 22 Copynumber: 2.1 Consensus size: 20
1476911 CAAAATATAT
1476921 AATATATATAAA-TTTTGAA
1 AATATATATAAATTTTTGAA
*
1476940 AATATATAGTATAGTTTTTGAA
1 AATATATA-TA-AATTTTTGAA
1476962 AA
1 AA
1476964 CACGAATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 8 0.40
20 2 0.10
21 1 0.05
22 9 0.45
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.42
Consensus pattern (20 bp):
AATATATATAAATTTTTGAA
Found at i:1477073 original size:37 final size:37
Alignment explanation
Indices: 1476970--1477161 Score: 127
Period size: 37 Copynumber: 4.8 Consensus size: 37
1476960 AAAACACGAA
* * *
1476970 TTTAAAAACGTATAATATATAGTTTTCTTAAAAATTGTTTTT
1 TTTAAAAACATATAATATATAGTTTT-TT-AAAA-CG--GTT
* * * *
1477012 TTTAACATATATATATATAATATAGTCTTTGAAAAC-GTAT
1 TTTAA-AAACATATA-AT-ATATAGTTTTTTAAAACGGT-T
1477052 TTTAAAAACATATAATATATAGTTTTTTAAAACGGTT
1 TTTAAAAACATATAATATATAGTTTTTTAAAACGGTT
* * * *
1477089 TTTGAAAATATATAACATATAGTTTTTTAAAAAAATGGTT
1 TTTAAAAACATATAATATATAGTTTTTT---AAAACGGTT
*
1477129 TTTGGAAAACATAT-ATAATATAGTTTTTATAAA
1 TTT-AAAAACATATAAT-ATATAGTTTTT-TAAA
1477162 CATATTTTTA
Statistics
Matches: 122, Mismatches: 17, Indels: 25
0.74 0.10 0.15
Matches are distributed among these distances:
37 41 0.34
38 4 0.03
39 11 0.09
40 18 0.15
41 20 0.16
42 6 0.05
43 10 0.08
44 3 0.02
45 9 0.07
ACGTcount: A:0.43, C:0.05, G:0.08, T:0.44
Consensus pattern (37 bp):
TTTAAAAACATATAATATATAGTTTTTTAAAACGGTT
Found at i:1477109 original size:83 final size:83
Alignment explanation
Indices: 1476941--1477102 Score: 197
Period size: 82 Copynumber: 2.0 Consensus size: 83
1476931 AATTTTGAAA
* * * **
1476941 ATATATAGTATAGTTTTTGAAAACACGAATTTAAAAACGTATAATATATAGTTTTCTTAAAAATT
1 ATATATAATATAGTCTTTGAAAACACGAATTTAAAAACATATAATATATAGTTTTCTTAAAAACG
***
1477006 GTTTTTTTTAACATATAT
66 GTTTTTGAAAACATATAT
*
1477024 ATATATAATATAGTCTTTG-AAA-ACGTATTTTAAAAACATATAATATATAGTTTT-TT-AAAAC
1 ATATATAATATAGTCTTTGAAAACACG-AATTTAAAAACATATAATATATAGTTTTCTTAAAAAC
*
1477085 GGTTTTTGAAAATATATA
65 GGTTTTTGAAAACATATA
1477103 ACATATAGTT
Statistics
Matches: 68, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
80 17 0.25
81 5 0.07
82 29 0.43
83 17 0.25
ACGTcount: A:0.43, C:0.06, G:0.09, T:0.43
Consensus pattern (83 bp):
ATATATAATATAGTCTTTGAAAACACGAATTTAAAAACATATAATATATAGTTTTCTTAAAAACG
GTTTTTGAAAACATATAT
Found at i:1477150 original size:41 final size:40
Alignment explanation
Indices: 1477043--1477161 Score: 131
Period size: 37 Copynumber: 3.0 Consensus size: 40
1477033 ATAGTCTTTG
* *
1477043 AAAAC-GTATTTTAAAAACATATAATATATAGTTTTTT---
1 AAAACGGT-TTTTGAAAACATATAACATATAGTTTTTTAAA
*
1477080 AAAACGGTTTTTGAAAATATATAACATATAGTTTTTTAAA
1 AAAACGGTTTTTGAAAACATATAACATATAGTTTTTTAAA
*
1477120 AAAATGGTTTTTGGAAAACATATATA-ATATAGTTTTTATAAA
1 AAAACGGTTTTT-GAAAACATATA-ACATATAGTTTTT-TAAA
1477162 CATATTTTTA
Statistics
Matches: 70, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
37 31 0.44
38 2 0.03
40 11 0.16
41 21 0.30
42 5 0.07
ACGTcount: A:0.45, C:0.04, G:0.09, T:0.41
Consensus pattern (40 bp):
AAAACGGTTTTTGAAAACATATAACATATAGTTTTTTAAA
Found at i:1477174 original size:25 final size:25
Alignment explanation
Indices: 1477170--1477229 Score: 57
Period size: 29 Copynumber: 2.2 Consensus size: 25
1477160 AACATATTTT
* * *
1477170 TATATAATTTTGAAAATATATAATA
1 TATATAGTTTTTAAAACATATAATA
1477195 TATATAGTTTTTGAAAAACATATGTAATA
1 TATATAGTTTTT--AAAACATA--TAATA
1477224 TATATA
1 TATATA
1477230 TATATATATT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
25 10 0.36
27 7 0.25
29 11 0.39
ACGTcount: A:0.48, C:0.02, G:0.07, T:0.43
Consensus pattern (25 bp):
TATATAGTTTTTAAAACATATAATA
Found at i:1477246 original size:33 final size:36
Alignment explanation
Indices: 1477184--1477250 Score: 104
Period size: 33 Copynumber: 1.9 Consensus size: 36
1477174 TAATTTTGAA
*
1477184 AATATATAATATATATAGTTTTTGAAAAACATATGT
1 AATATATAATATATATAGTATTTGAAAAACATATGT
1477220 AATATAT-ATATATATA-TATTTG-AAAACATAT
1 AATATATAATATATATAGTATTTGAAAAACATAT
1477251 TATATGATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 9 0.30
34 5 0.17
35 9 0.30
36 7 0.23
ACGTcount: A:0.49, C:0.03, G:0.06, T:0.42
Consensus pattern (36 bp):
AATATATAATATATATAGTATTTGAAAAACATATGT
Found at i:1477254 original size:19 final size:21
Alignment explanation
Indices: 1477227--1477276 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
1477217 TGTAATATAT
1477227 ATATATATAT-ATTT-GAAAAC
1 ATAT-TATATGATTTCGAAAAC
*
1477247 ATATTATATGATTTCGAAAAT
1 ATATTATATGATTTCGAAAAC
*
1477268 ATAATATAT
1 ATATTATAT
1477277 TATATAGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 5 0.19
20 8 0.31
21 13 0.50
ACGTcount: A:0.48, C:0.04, G:0.06, T:0.42
Consensus pattern (21 bp):
ATATTATATGATTTCGAAAAC
Found at i:1477254 original size:21 final size:21
Alignment explanation
Indices: 1477225--1477281 Score: 53
Period size: 21 Copynumber: 2.6 Consensus size: 21
1477215 TATGTAATAT
*
1477225 ATATATATATATATTTGAAAAC
1 ATAT-TATATATATTCGAAAAC
*
1477247 ATATTATATGAT-TTCGAAAAT
1 ATATTATAT-ATATTCGAAAAC
*
1477268 ATAATATATTATAT
1 ATATTATA-TATAT
1477282 AGTTTTTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
21 21 0.72
22 8 0.28
ACGTcount: A:0.47, C:0.04, G:0.05, T:0.44
Consensus pattern (21 bp):
ATATTATATATATTCGAAAAC
Found at i:1478471 original size:32 final size:31
Alignment explanation
Indices: 1478434--1478495 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 31
1478424 TGAAATCCTT
*
1478434 TTAATTTAAAGTTTTATTTTACTTT-ATATTTC
1 TTAATTT-AA-TTTTATCTTACTTTAATATTTC
*
1478466 TTAATTTAATTTTGTCTTACTTTAATATTT
1 TTAATTTAATTTTATCTTACTTTAATATTT
1478496 AAAACTAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
30 12 0.44
31 8 0.30
32 7 0.26
ACGTcount: A:0.27, C:0.06, G:0.03, T:0.63
Consensus pattern (31 bp):
TTAATTTAATTTTATCTTACTTTAATATTTC
Found at i:1478489 original size:16 final size:15
Alignment explanation
Indices: 1478452--1478495 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
1478442 AAGTTTTATT
1478452 TTACTTT-ATATTTC
1 TTACTTTAATATTTC
* *
1478466 TTAATTTAATTTTGTC
1 TTACTTTAATATT-TC
1478482 TTACTTTAATATTT
1 TTACTTTAATATTT
1478496 AAAACTAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
14 6 0.25
15 5 0.21
16 13 0.54
ACGTcount: A:0.25, C:0.09, G:0.02, T:0.64
Consensus pattern (15 bp):
TTACTTTAATATTTC
Found at i:1479575 original size:18 final size:17
Alignment explanation
Indices: 1479552--1479585 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1479542 TCTTACTAAC
1479552 TTGTTTCCTTCTTATTTG
1 TTGTTTCCTT-TTATTTG
*
1479570 TTGTTTTCTTTTATTT
1 TTGTTTCCTTTTATTT
1479586 TTTTTCTCCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.06, C:0.12, G:0.09, T:0.74
Consensus pattern (17 bp):
TTGTTTCCTTTTATTTG
Found at i:1485913 original size:31 final size:30
Alignment explanation
Indices: 1485878--1485935 Score: 89
Period size: 31 Copynumber: 1.9 Consensus size: 30
1485868 TAAATTACAA
*
1485878 ATTTAATATTTAAACTATTAATTTTTTATTC
1 ATTTAATATCTAAACT-TTAATTTTTTATTC
*
1485909 ATTTAATATCTAAACTTTCATTTTTTA
1 ATTTAATATCTAAACTTTAATTTTTTA
1485936 AAAATATACC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 10 0.40
31 15 0.60
ACGTcount: A:0.34, C:0.09, G:0.00, T:0.57
Consensus pattern (30 bp):
ATTTAATATCTAAACTTTAATTTTTTATTC
Found at i:1486870 original size:31 final size:31
Alignment explanation
Indices: 1486805--1486894 Score: 132
Period size: 31 Copynumber: 3.0 Consensus size: 31
1486795 ATATGATCAC
*
1486805 TTTTAATTTTATTTAATTAATAA-G-A-TCAA
1 TTTTATTTTTATTTAATTAA-AATGTAGTCAA
*
1486834 TTTTATTTTTATTTAATTAAAATGTAGTTAA
1 TTTTATTTTTATTTAATTAAAATGTAGTCAA
1486865 TTTTATTTTTATTTAATTAAAATGTAGTCA
1 TTTTATTTTTATTTAATTAAAATGTAGTCA
1486895 CCACGGGTTA
Statistics
Matches: 55, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
28 2 0.04
29 20 0.36
30 1 0.02
31 32 0.58
ACGTcount: A:0.37, C:0.02, G:0.06, T:0.56
Consensus pattern (31 bp):
TTTTATTTTTATTTAATTAAAATGTAGTCAA
Found at i:1487381 original size:17 final size:17
Alignment explanation
Indices: 1487361--1487394 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1487351 TTATATTAAT
1487361 TTATTAA-ATATATTTTA
1 TTATTAACATA-ATTTTA
1487378 TTATTAACATAATTTTA
1 TTATTAACATAATTTTA
1487395 AAATATTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.81
18 3 0.19
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (17 bp):
TTATTAACATAATTTTA
Found at i:1487382 original size:25 final size:23
Alignment explanation
Indices: 1487310--1487384 Score: 73
Period size: 23 Copynumber: 3.1 Consensus size: 23
1487300 ACTTAACTTA
1487310 AATTTAT-AATATTTTATATATATT
1 AATTTATAAATATTTT-TAT-TATT
*
1487334 AAATTTAAGAAATATTTTTA-TATT
1 -AATTT-ATAAATATTTTTATTATT
1487358 AATTTATTAAATATATTTTATTATT
1 AATTTA-TAAATAT-TTTTATTATT
1487383 AA
1 AA
1487385 CATAATTTTA
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
22 1 0.02
23 11 0.26
24 9 0.21
25 11 0.26
26 3 0.07
27 8 0.19
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (23 bp):
AATTTATAAATATTTTTATTATT
Found at i:1487647 original size:25 final size:23
Alignment explanation
Indices: 1487615--1487686 Score: 74
Period size: 24 Copynumber: 2.9 Consensus size: 23
1487605 TTTTTTAAAT
1487615 TAAGTTAATAATAAAATATATTTAA
1 TAAGTTAATAATAAAA-ATATTT-A
*
1487640 TAAGTTAAT-ATAAAAATTATTTT
1 TAAGTTAATAATAAAAA-TATTTA
1487663 TAAAGTTAATATATAAAAAATATT
1 T-AAGTTAATA-AT-AAAAATATT
1487687 ATGAATTAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
23 2 0.05
24 19 0.46
25 9 0.22
26 6 0.15
27 5 0.12
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (23 bp):
TAAGTTAATAATAAAAATATTTA
Found at i:1487660 original size:24 final size:25
Alignment explanation
Indices: 1487615--1487686 Score: 87
Period size: 25 Copynumber: 2.9 Consensus size: 25
1487605 TTTTTTAAAT
1487615 TAAGTTAATA-ATAAAATATATTTAA
1 TAAGTTAATATATAAAATATATTT-A
*
1487640 TAAGTTAATATA-AAAAT-TATTTT
1 TAAGTTAATATATAAAATATATTTA
*
1487663 TAAAGTTAATATATAAAAAATATT
1 T-AAGTTAATATATAAAATATATT
1487687 ATGAATTAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
23 1 0.02
24 16 0.39
25 19 0.46
26 5 0.12
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (25 bp):
TAAGTTAATATATAAAATATATTTA
Found at i:1487676 original size:26 final size:26
Alignment explanation
Indices: 1487615--1487686 Score: 80
Period size: 26 Copynumber: 2.8 Consensus size: 26
1487605 TTTTTTAAAT
1487615 TAAGTTAATA-AT-AAAATATATTTAA
1 TAAGTTAATATATAAAAATAT-TTTAA
* *
1487640 TAAGTTAATATA-AAAATTATTTTTA
1 TAAGTTAATATATAAAAATATTTTAA
1487665 -AAGTTAATATATAAAAAATATT
1 TAAGTTAATATAT-AAAAATATT
1487687 ATGAATTAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
24 11 0.28
25 14 0.35
26 15 0.38
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (26 bp):
TAAGTTAATATATAAAAATATTTTAA
Found at i:1492321 original size:37 final size:36
Alignment explanation
Indices: 1492287--1492363 Score: 93
Period size: 37 Copynumber: 2.1 Consensus size: 36
1492277 TTTTTATATT
*
1492287 TTTAATTTTGTAAA-AATATTTATATAAATATTATAAA
1 TTTAATTTTGTAAAGAA-A-ATATATAAATATTATAAA
* *
1492324 TTTAATTTTTTAAAGAAAATATATAAATATTTTACAA
1 TTTAATTTTGTAAAGAAAATATATAAATATTATA-AA
1492361 TTT
1 TTT
1492364 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
36 14 0.40
37 19 0.54
38 2 0.06
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.49
Consensus pattern (36 bp):
TTTAATTTTGTAAAGAAAATATATAAATATTATAAA
Found at i:1492546 original size:20 final size:20
Alignment explanation
Indices: 1492510--1492547 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1492500 ATCCTATTCC
**
1492510 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
1492530 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
1492548 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:1495569 original size:13 final size:13
Alignment explanation
Indices: 1495535--1495569 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
1495525 TTATATTTTT
1495535 AAAATAAAATAAA
1 AAAATAAAATAAA
*
1495548 AAAACAAAATAAA
1 AAAATAAAATAAA
*
1495561 AACATAAAA
1 AAAATAAAA
1495570 ATATAAGTGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.83, C:0.06, G:0.00, T:0.11
Consensus pattern (13 bp):
AAAATAAAATAAA
Found at i:1498074 original size:4 final size:4
Alignment explanation
Indices: 1498065--1498089 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1498055 AGATGGTAAT
1498065 AGGA AGGA AGGA AGGA AGGA AGGA A
1 AGGA AGGA AGGA AGGA AGGA AGGA A
1498090 AGGGTTAGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (4 bp):
AGGA
Found at i:1503836 original size:31 final size:31
Alignment explanation
Indices: 1503800--1503908 Score: 209
Period size: 31 Copynumber: 3.5 Consensus size: 31
1503790 GAATAAATTT
*
1503800 CTTGTTCATGTTCATTTAGTAAGAAATTTAG
1 CTTGTTCGTGTTCATTTAGTAAGAAATTTAG
1503831 CTTGTTCGTGTTCATTTAGTAAGAAATTTAG
1 CTTGTTCGTGTTCATTTAGTAAGAAATTTAG
1503862 CTTGTTCGTGTTCATTTAGTAAGAAATTTAG
1 CTTGTTCGTGTTCATTTAGTAAGAAATTTAG
1503893 CTTGTTCGTGTTCATT
1 CTTGTTCGTGTTCATT
1503909 CATTATTTTT
Statistics
Matches: 77, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
31 77 1.00
ACGTcount: A:0.24, C:0.11, G:0.18, T:0.47
Consensus pattern (31 bp):
CTTGTTCGTGTTCATTTAGTAAGAAATTTAG
Found at i:1503993 original size:14 final size:14
Alignment explanation
Indices: 1503956--1503994 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
1503946 AAAAAAACGT
* *
1503956 AAACGAACACAAAT
1 AAACGAACATAAAC
*
1503970 AAAGGAACATAAAC
1 AAACGAACATAAAC
1503984 AAACGAACATA
1 AAACGAACATA
1503995 TTTTTTTGAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.64, C:0.18, G:0.10, T:0.08
Consensus pattern (14 bp):
AAACGAACATAAAC
Found at i:1504226 original size:37 final size:37
Alignment explanation
Indices: 1504184--1504254 Score: 108
Period size: 37 Copynumber: 1.9 Consensus size: 37
1504174 AATAAACGAA
1504184 TGAACATAAACT-AACATAAACAAACAAACATAAAAAT
1 TGAACATAAA-TGAACATAAACAAACAAACATAAAAAT
* *
1504221 TGAACATAAATGAACATAAATAAACGAACATAAA
1 TGAACATAAATGAACATAAACAAACAAACATAAA
1504255 CGAACATATT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
36 1 0.03
37 30 0.97
ACGTcount: A:0.63, C:0.14, G:0.06, T:0.17
Consensus pattern (37 bp):
TGAACATAAATGAACATAAACAAACAAACATAAAAAT
Found at i:1504249 original size:14 final size:14
Alignment explanation
Indices: 1504189--1504254 Score: 52
Period size: 14 Copynumber: 5.1 Consensus size: 14
1504179 ACGAATGAAC
*
1504189 ATAAACTAACATAA
1 ATAAACGAACATAA
* *
1504203 ACAAACAAACATAA
1 ATAAACGAACATAA
**
1504217 A-AATTGAACATAA
1 ATAAACGAACATAA
1504230 AT----GAACATAA
1 ATAAACGAACATAA
1504240 ATAAACGAACATAA
1 ATAAACGAACATAA
1504254 A
1 A
1504255 CGAACATATT
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
10 10 0.24
13 10 0.24
14 22 0.52
ACGTcount: A:0.65, C:0.14, G:0.05, T:0.17
Consensus pattern (14 bp):
ATAAACGAACATAA
Found at i:1524276 original size:11 final size:10
Alignment explanation
Indices: 1524256--1524302 Score: 76
Period size: 10 Copynumber: 4.6 Consensus size: 10
1524246 GATAAAAATG
1524256 AAAAAATGAA
1 AAAAAATGAA
1524266 AAAAAATTGAA
1 AAAAAA-TGAA
*
1524277 AAAAAATAAA
1 AAAAAATGAA
1524287 AAAAAATGAA
1 AAAAAATGAA
1524297 AAAAAA
1 AAAAAA
1524303 CGAATAAAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
10 24 0.71
11 10 0.29
ACGTcount: A:0.83, C:0.00, G:0.06, T:0.11
Consensus pattern (10 bp):
AAAAAATGAA
Found at i:1524311 original size:20 final size:20
Alignment explanation
Indices: 1524256--1524302 Score: 76
Period size: 21 Copynumber: 2.3 Consensus size: 20
1524246 GATAAAAATG
1524256 AAAAAATGAAAAAAAATTGAA
1 AAAAAATGAAAAAAAA-TGAA
*
1524277 AAAAAATAAAAAAAAATGAA
1 AAAAAATGAAAAAAAATGAA
1524297 AAAAAA
1 AAAAAA
1524303 CGAATAAAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 10 0.40
21 15 0.60
ACGTcount: A:0.83, C:0.00, G:0.06, T:0.11
Consensus pattern (20 bp):
AAAAAATGAAAAAAAATGAA
Found at i:1525413 original size:55 final size:55
Alignment explanation
Indices: 1525347--1525764 Score: 469
Period size: 55 Copynumber: 7.7 Consensus size: 55
1525337 TTGAAACATT
* * * **
1525347 AAGATTGTTTGAGTCTTATACTCTCTGAAGGAATATGGAGCAGACACAATTGTTG
1 AAGATTGTTCGAGTCCTATACTCTCTGAAGGAATAGGGAGCAGACACGTTTGTTG
* * *
1525402 AAGATTGTTTGAGTCTTATACTCTCTGAAGGAATAGGGAGCGGACACGTTTGTTG
1 AAGATTGTTCGAGTCCTATACTCTCTGAAGGAATAGGGAGCAGACACGTTTGTTG
* **
1525457 AAGATTGTTCAAGTCCTATACTCTCTGAAGGAATAGGGAGTGGACACGTTTGTTG
1 AAGATTGTTCGAGTCCTATACTCTCTGAAGGAATAGGGAGCAGACACGTTTGTTG
* * * *
1525512 AAGGTTGTTCAAGTCATATACTCTCTGAAGAAATAGGGAGC-GAACACGTTTGTTG
1 AAGATTGTTCGAGTCCTATACTCTCTGAAGGAATAGGGAGCAG-ACACGTTTGTTG
* *
1525567 AAGA---TT-GAGTCCTATACTCTCTAAAGGAATAGGGAGCATACACGTTTGTTG
1 AAGATTGTTCGAGTCCTATACTCTCTGAAGGAATAGGGAGCAGACACGTTTGTTG
* * * *
1525618 AAGGTTGTTCAAGTCCTATACTCTCTGAAGAAATAGGGAGCAAACACGTTTGTTG
1 AAGATTGTTCGAGTCCTATACTCTCTGAAGGAATAGGGAGCAGACACGTTTGTTG
* * *
1525673 AAGA----TCGAGTCCTATACTCTCTGAAGGAATAGGGAACAAACATGTTT-TATG
1 AAGATTGTTCGAGTCCTATACTCTCTGAAGGAATAGGGAGCAGACACGTTTGT-TG
** ** * * *
1525724 AAGATTGTTATAGTTTTATACTCCCTGAAGCAAGAGGGAGC
1 AAGATTGTTCGAGTCCTATACTCTCTGAAGGAATAGGGAGC
1525765 GAACCCGATG
Statistics
Matches: 316, Mismatches: 36, Indels: 22
0.84 0.10 0.06
Matches are distributed among these distances:
50 1 0.00
51 87 0.28
52 2 0.01
54 3 0.01
55 223 0.71
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.30
Consensus pattern (55 bp):
AAGATTGTTCGAGTCCTATACTCTCTGAAGGAATAGGGAGCAGACACGTTTGTTG
Found at i:1525626 original size:106 final size:106
Alignment explanation
Indices: 1525355--1525768 Score: 535
Period size: 106 Copynumber: 3.9 Consensus size: 106
1525345 TTAAGATTGT
* * ** **
1525355 TTGAGTCTTATACTCTCTGAAGGAATATGGAGCAGACACAATTGTTGAAGATTGTTTGAGTCTTA
1 TTGAGTCCTATACTCTCTGAAGGAATAGGGAGCAGACACGTTTGTTGAAGATTGTTCAAGTCTTA
* *
1525420 TACTCTCTGAAGGAATAGGGAGCGGACACGTTTGTTGAAGA
66 TACTCTCTGAAGAAATAGGGAGCGAACACGTTTGTTGAAGA
** *
1525461 TTGTTCAAGTCCTATACTCTCTGAAGGAATAGGGAGTGGACACGTTTGTTGAAGGTTGTTCAAGT
1 TTG----AGTCCTATACTCTCTGAAGGAATAGGGAGCAGACACGTTTGTTGAAGATTGTTCAAGT
*
1525526 CATATACTCTCTGAAGAAATAGGGAGCGAACACGTTTGTTGAAGA
62 CTTATACTCTCTGAAGAAATAGGGAGCGAACACGTTTGTTGAAGA
* * * *
1525571 TTGAGTCCTATACTCTCTAAAGGAATAGGGAGCATACACGTTTGTTGAAGGTTGTTCAAGTCCTA
1 TTGAGTCCTATACTCTCTGAAGGAATAGGGAGCAGACACGTTTGTTGAAGATTGTTCAAGTCTTA
*
1525636 TACTCTCTGAAGAAATAGGGAGCAAACACGTTTGTTGAAGA
66 TACTCTCTGAAGAAATAGGGAGCGAACACGTTTGTTGAAGA
* * * * *
1525677 TCGAGTCCTATACTCTCTGAAGGAATAGGGAACAAACATGTTT-TATGAAGATTGTT-ATAGTTT
1 TTGAGTCCTATACTCTCTGAAGGAATAGGGAGCAGACACGTTTGT-TGAAGATTGTTCA-AGTCT
* * *
1525740 TATACTCCCTGAAGCAAGAGGGAGCGAAC
64 TATACTCTCTGAAGAAATAGGGAGCGAAC
1525769 CCGATGGTCG
Statistics
Matches: 272, Mismatches: 30, Indels: 12
0.87 0.10 0.04
Matches are distributed among these distances:
105 2 0.01
106 176 0.65
110 94 0.35
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.30
Consensus pattern (106 bp):
TTGAGTCCTATACTCTCTGAAGGAATAGGGAGCAGACACGTTTGTTGAAGATTGTTCAAGTCTTA
TACTCTCTGAAGAAATAGGGAGCGAACACGTTTGTTGAAGA
Found at i:1525746 original size:161 final size:159
Alignment explanation
Indices: 1525357--1525764 Score: 482
Period size: 161 Copynumber: 2.5 Consensus size: 159
1525347 AAGATTGTTT
* * * *
1525357 GAGTCTTATACTCTCTGAAGGAATATGGAGCAGACACAATTGTTGAAGATTGTTTGAGTCTTATA
1 GAGTCATATACTCTCTGAAGGAATAGGGAGCA-A-ACAGTTTTTGAAGATTGTTT-AGTCTTATA
*
1525422 CTCTCTGAAGGAATAGGGAGCGGACACGTTTGTTGAAGATTGTTCAAGTCCTATACTCTCTGAAG
63 CTCTCTGAAGGAATAGGGAGCAGACACGTTTGTTGAAGATTGTTCAAGTCCTATACTCTCTGAAG
* *** *
1525487 GAATAGGGAGTGGACACGTTTGTTGAAGGTTGTTC
128 AAATAGGGAGCAAACACGTTTGTTGAA-G--GATC
* * * *
1525522 AAGTCATATACTCTCTGAAGAAATAGGGAGCGAACACGTTTGTTGAAGATTG---AGTCCTATAC
1 GAGTCATATACTCTCTGAAGGAATAGGGAGCAAACA-GTTT-TTGAAGATTGTTTAGTCTTATAC
* * *
1525584 TCTCTAAAGGAATAGGGAGCATACACGTTTGTTGAAGGTTGTTCAAGTCCTATACTCTCTGAAGA
64 TCTCTGAAGGAATAGGGAGCAGACACGTTTGTTGAAGATTGTTCAAGTCCTATACTCTCTGAAGA
1525649 AATAGGGAGCAAACACGTTTGTTGAA-GATC
129 AATAGGGAGCAAACACGTTTGTTGAAGGATC
* * *
1525679 GAGTCCTATACTCTCTGAAGGAATAGGGAACAAACATGTTTTATGAAGATTGTTATAGTTTTATA
1 GAGTCATATACTCTCTGAAGGAATAGGGAGCAAACA-GTTTT-TGAAGATTGTT-TAGTCTTATA
* * *
1525744 CTCCCTGAAGCAAGAGGGAGC
63 CTCTCTGAAGGAATAGGGAGC
1525765 GAACCCGATG
Statistics
Matches: 207, Mismatches: 29, Indels: 18
0.81 0.11 0.07
Matches are distributed among these distances:
156 1 0.00
157 47 0.23
161 116 0.56
163 3 0.01
164 3 0.01
165 37 0.18
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.30
Consensus pattern (159 bp):
GAGTCATATACTCTCTGAAGGAATAGGGAGCAAACAGTTTTTGAAGATTGTTTAGTCTTATACTC
TCTGAAGGAATAGGGAGCAGACACGTTTGTTGAAGATTGTTCAAGTCCTATACTCTCTGAAGAAA
TAGGGAGCAAACACGTTTGTTGAAGGATC
Found at i:1525982 original size:3 final size:3
Alignment explanation
Indices: 1525969--1526006 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
1525959 ATTATATATT
*
1525969 ATA ACA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1526007 TATTATTATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1531276 original size:12 final size:12
Alignment explanation
Indices: 1531259--1531287 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
1531249 TTGTTGTGCT
1531259 TGCTCCTCGGGC
1 TGCTCCTCGGGC
1531271 TGCTCCTCGGGC
1 TGCTCCTCGGGC
1531283 TGCTC
1 TGCTC
1531288 AGGCTCATCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.00, C:0.41, G:0.31, T:0.28
Consensus pattern (12 bp):
TGCTCCTCGGGC
Found at i:1536797 original size:22 final size:21
Alignment explanation
Indices: 1536755--1536794 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1536745 GAGTTTATTT
*
1536755 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
1536776 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
1536795 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:1549027 original size:173 final size:173
Alignment explanation
Indices: 1548733--1549079 Score: 658
Period size: 173 Copynumber: 2.0 Consensus size: 173
1548723 AAAAGACATT
* *
1548733 AATTTTGTAGAGACTTCTTCTTTGGTTTCATTAAAAGACTCTTTTAGGATAATCATGATACTTGT
1 AATTTTGTAGAGACTTCCTCTTTGGTTTCATTAAAAGACTCTTTTAGGATAATCATGATAATTGT
1548798 TTTTATCTAGAGTTACATAAATTGTATTTCAAAATTATGTTTCTCAATGATAACATTGATGAGAT
66 TTTTATCTAGAGTTACATAAATTGTATTTCAAAATTATGTTTCTCAATGATAACATTGATGAGAT
1548863 ATTTTATATGGTGTAATTAAAAAATTATATCTGATGATAGAAA
131 ATTTTATATGGTGTAATTAAAAAATTATATCTGATGATAGAAA
*
1548906 AATTTTGTAGAGACTTCCTCTTTGGTTTCATTGAAAGACTCTTTTAGGATAATCATGATAATTGT
1 AATTTTGTAGAGACTTCCTCTTTGGTTTCATTAAAAGACTCTTTTAGGATAATCATGATAATTGT
*
1548971 TTTTATCTAGAGTTACATAAATTGTATTTCAAAATTATGTTTCTCAATGGTAACATTGATGAGAT
66 TTTTATCTAGAGTTACATAAATTGTATTTCAAAATTATGTTTCTCAATGATAACATTGATGAGAT
1549036 ATTTTATATGGTGTAATTAAAAAATTATATCTGATGATAGAAA
131 ATTTTATATGGTGTAATTAAAAAATTATATCTGATGATAGAAA
1549079 A
1 A
1549080 TTAATGATAC
Statistics
Matches: 170, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
173 170 1.00
ACGTcount: A:0.35, C:0.09, G:0.14, T:0.42
Consensus pattern (173 bp):
AATTTTGTAGAGACTTCCTCTTTGGTTTCATTAAAAGACTCTTTTAGGATAATCATGATAATTGT
TTTTATCTAGAGTTACATAAATTGTATTTCAAAATTATGTTTCTCAATGATAACATTGATGAGAT
ATTTTATATGGTGTAATTAAAAAATTATATCTGATGATAGAAA
Found at i:1549741 original size:18 final size:19
Alignment explanation
Indices: 1549727--1549762 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1549717 GTAAAAAGCG
*
1549727 ATTAAA-TAAATAAAAGAA
1 ATTAAAGTAAAAAAAAGAA
1549745 ATTAAAGTAAAAAAAAGA
1 ATTAAAGTAAAAAAAAGA
1549763 GGGTAAAGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.72, C:0.00, G:0.08, T:0.19
Consensus pattern (19 bp):
ATTAAAGTAAAAAAAAGAA
Found at i:1552425 original size:30 final size:30
Alignment explanation
Indices: 1552391--1552458 Score: 109
Period size: 30 Copynumber: 2.3 Consensus size: 30
1552381 GACCAAATAA
* *
1552391 AATTAGTTTGATTAATTCGGTTGGCCATCG
1 AATTAGTTTGATTAATTCGGTCGGCCACCG
*
1552421 AATTAGTTTGGTTAATTCGGTCGGCCACCG
1 AATTAGTTTGATTAATTCGGTCGGCCACCG
1552451 AATTAGTT
1 AATTAGTT
1552459 CGGTCGGGGA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.24, C:0.15, G:0.24, T:0.38
Consensus pattern (30 bp):
AATTAGTTTGATTAATTCGGTCGGCCACCG
Found at i:1552590 original size:15 final size:15
Alignment explanation
Indices: 1552570--1552598 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1552560 AAAAAAAATT
1552570 TGGTTAATTCGGTTA
1 TGGTTAATTCGGTTA
1552585 TGGTTAATTCGGTT
1 TGGTTAATTCGGTT
1552599 TAGTCGGTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.07, G:0.28, T:0.48
Consensus pattern (15 bp):
TGGTTAATTCGGTTA
Found at i:1556591 original size:8 final size:8
Alignment explanation
Indices: 1556578--1556606 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
1556568 TATCCCTATT
1556578 TTTTAATA
1 TTTTAATA
1556586 TTTTAATA
1 TTTTAATA
1556594 TTTTAATA
1 TTTTAATA
1556602 TTTTA
1 TTTTA
1556607 TTTTAAGATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (8 bp):
TTTTAATA
Found at i:1556906 original size:2 final size:2
Alignment explanation
Indices: 1556899--1556944 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
1556889 AAGTACATAC
*
1556899 AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1556941 AT AT
1 AT AT
1556945 TAATAAAAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1559901 original size:31 final size:30
Alignment explanation
Indices: 1559831--1559889 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 30
1559821 AAAAAATATA
* *
1559831 ATATAACTTTCGTTTTTGTTTAATTAAGTT
1 ATATCACTTTCGTTTTTATTTAATTAAGTT
1559861 ATGATCACTTTCGTTTTTATTTAATTAAG
1 AT-ATCACTTTCGTTTTTATTTAATTAAG
1559890 ATGTATTCAC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 2 0.08
31 24 0.92
ACGTcount: A:0.27, C:0.08, G:0.10, T:0.54
Consensus pattern (30 bp):
ATATCACTTTCGTTTTTATTTAATTAAGTT
Found at i:1571622 original size:14 final size:15
Alignment explanation
Indices: 1571595--1571627 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
1571585 ATTCATAGAT
1571595 AAAAAGAAAAAAAAG
1 AAAAAGAAAAAAAAG
*
1571610 AAAAAG-AATAAAAG
1 AAAAAGAAAAAAAAG
1571624 AAAA
1 AAAA
1571628 TATTAAGAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.85, C:0.00, G:0.12, T:0.03
Consensus pattern (15 bp):
AAAAAGAAAAAAAAG
Found at i:1575761 original size:39 final size:39
Alignment explanation
Indices: 1575706--1575787 Score: 103
Period size: 39 Copynumber: 2.1 Consensus size: 39
1575696 AAGTTAATTT
* * * *
1575706 ATTTCTCTGAAAATATCGTGTATTTTTAGG-GTCTTCTTC
1 ATTTATCTGAAAATATCATGTAGTTGT-GGAGTCTTCTTC
*
1575745 ATTTATCTGAAGATATCATGTAGTTGTGGAGTCTTCTTC
1 ATTTATCTGAAAATATCATGTAGTTGTGGAGTCTTCTTC
1575784 ATTT
1 ATTT
1575788 TCATAAAGAT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
38 2 0.05
39 35 0.95
ACGTcount: A:0.22, C:0.13, G:0.17, T:0.48
Consensus pattern (39 bp):
ATTTATCTGAAAATATCATGTAGTTGTGGAGTCTTCTTC
Found at i:1581571 original size:36 final size:37
Alignment explanation
Indices: 1581525--1581597 Score: 112
Period size: 36 Copynumber: 2.0 Consensus size: 37
1581515 AGATCAAATC
*
1581525 TGGTTTGAATTTAGTTAAAGTC-TGAAAATTTAGTTA
1 TGGTTCGAATTTAGTTAAAGTCATGAAAATTTAGTTA
*
1581561 TGGTTCGAATTTAGTTAGAGTCTATGAAAATTTAGTT
1 TGGTTCGAATTTAGTTAAAGTC-ATGAAAATTTAGTT
1581598 CAGATCGGGT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
36 20 0.61
38 13 0.39
ACGTcount: A:0.32, C:0.04, G:0.21, T:0.44
Consensus pattern (37 bp):
TGGTTCGAATTTAGTTAAAGTCATGAAAATTTAGTTA
Found at i:1581780 original size:20 final size:20
Alignment explanation
Indices: 1581755--1581794 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1581745 GTTTCAATTT
* *
1581755 GGGTCAGCCCTTATATTTTC
1 GGGTCAACCCTTAGATTTTC
*
1581775 GGGTCAACCTTTAGATTTTC
1 GGGTCAACCCTTAGATTTTC
1581795 AGATCAATCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.17, C:0.23, G:0.20, T:0.40
Consensus pattern (20 bp):
GGGTCAACCCTTAGATTTTC
Found at i:1584371 original size:21 final size:22
Alignment explanation
Indices: 1584342--1584388 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 22
1584332 ATTCTGACTA
1584342 TCGCATTGCGATTTTCC-AAAT
1 TCGCATTGCGATTTTCCTAAAT
*
1584363 TCGCGTTGCGATTTTCCTAAA-
1 TCGCATTGCGATTTTCCTAAAT
1584384 TCGCA
1 TCGCA
1584389 ATACGAATAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 20 0.87
22 3 0.13
ACGTcount: A:0.21, C:0.26, G:0.17, T:0.36
Consensus pattern (22 bp):
TCGCATTGCGATTTTCCTAAAT
Found at i:1584405 original size:20 final size:20
Alignment explanation
Indices: 1584380--1584486 Score: 196
Period size: 20 Copynumber: 5.3 Consensus size: 20
1584370 GCGATTTTCC
*
1584380 TAAATCGCAATACGAATACG
1 TAAATCGCAATGCGAATACG
1584400 TAAATCGCAATGCGAATACG
1 TAAATCGCAATGCGAATACG
1584420 TAAATCGCAATGCGAATACG
1 TAAATCGCAATGCGAATACG
*
1584440 TAAATCACAATGCGAATACG
1 TAAATCGCAATGCGAATACG
1584460 TAAATCGCAATGCGAATACG
1 TAAATCGCAATGCGAATACG
1584480 TAAATCG
1 TAAATCG
1584487 TAATTATTAA
Statistics
Matches: 84, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 84 1.00
ACGTcount: A:0.42, C:0.20, G:0.18, T:0.21
Consensus pattern (20 bp):
TAAATCGCAATGCGAATACG
Found at i:1584529 original size:20 final size:19
Alignment explanation
Indices: 1584504--1584566 Score: 72
Period size: 20 Copynumber: 3.2 Consensus size: 19
1584494 TAATATGTAA
1584504 ATCACAACGCGAATCTGACT
1 ATCACAACG-GAATCTGACT
*
1584524 ATCACAACGAAATTCTGACT
1 ATCACAACGGAA-TCTGACT
* *
1584544 ATCGCAACGAGATTCTGACT
1 ATCACAACG-GAATCTGACT
1584564 ATC
1 ATC
1584567 GCAATACTGA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
19 2 0.05
20 34 0.92
21 1 0.03
ACGTcount: A:0.35, C:0.27, G:0.14, T:0.24
Consensus pattern (19 bp):
ATCACAACGGAATCTGACT
Found at i:1584567 original size:20 final size:20
Alignment explanation
Indices: 1584517--1584570 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
1584507 ACAACGCGAA
*
1584517 TCTGACTATCACAACGAAAT
1 TCTGACTATCGCAACGAAAT
*
1584537 TCTGACTATCGCAACGAGAT
1 TCTGACTATCGCAACGAAAT
1584557 TCTGACTATCGCAA
1 TCTGACTATCGCAA
1584571 TACTGAATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.33, C:0.26, G:0.15, T:0.26
Consensus pattern (20 bp):
TCTGACTATCGCAACGAAAT
Found at i:1587901 original size:20 final size:19
Alignment explanation
Indices: 1587876--1587969 Score: 125
Period size: 20 Copynumber: 4.7 Consensus size: 19
1587866 GACATTCATT
1587876 TGACTATCGCAACGCGAATA
1 TGACTATCGCAACGCGAA-A
*
1587896 TGACTATCGCAACAGGGAAA
1 TGACTATCGCAAC-GCGAAA
* *
1587916 TGACTATCGCAACGTGGAAT
1 TGACTATCGCAACG-CGAAA
1587936 TGACTATCGCAACGCAGAAA
1 TGACTATCGCAACGC-GAAA
1587956 TGACTATCGCAACG
1 TGACTATCGCAACG
1587970 AGAGAATCGC
Statistics
Matches: 67, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
19 1 0.01
20 62 0.93
21 4 0.06
ACGTcount: A:0.35, C:0.23, G:0.22, T:0.19
Consensus pattern (19 bp):
TGACTATCGCAACGCGAAA
Found at i:1587940 original size:40 final size:40
Alignment explanation
Indices: 1587876--1587969 Score: 138
Period size: 40 Copynumber: 2.4 Consensus size: 40
1587866 GACATTCATT
*
1587876 TGACTATCGCAACGCGAATATGACTATCGCAACAG-GGAAA
1 TGACTATCGCAACGCGAATATGACTATCGCAAC-GCAGAAA
*
1587916 TGACTATCGCAACGTGGAAT-TGACTATCGCAACGCAGAAA
1 TGACTATCGCAACG-CGAATATGACTATCGCAACGCAGAAA
1587956 TGACTATCGCAACG
1 TGACTATCGCAACG
1587970 AGAGAATCGC
Statistics
Matches: 50, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
39 1 0.02
40 45 0.90
41 4 0.08
ACGTcount: A:0.35, C:0.23, G:0.22, T:0.19
Consensus pattern (40 bp):
TGACTATCGCAACGCGAATATGACTATCGCAACGCAGAAA
Found at i:1587991 original size:33 final size:33
Alignment explanation
Indices: 1587941--1588036 Score: 129
Period size: 33 Copynumber: 2.8 Consensus size: 33
1587931 GGAATTGACT
* **
1587941 ATCGCAACGCAGAAATGACTATCGCAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
*
1587975 ATCGCAATGCGAAATGAAAATCACAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
1588008 ATCACAATGCGAAAATGAAAATCGCAACG
1 ATCGCAATGCG-AAATGAAAATCGCAACG
1588037 CGAATTTAGT
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
33 30 0.55
34 25 0.45
ACGTcount: A:0.46, C:0.21, G:0.21, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:1588108 original size:33 final size:34
Alignment explanation
Indices: 1588051--1588126 Score: 127
Period size: 33 Copynumber: 2.3 Consensus size: 34
1588041 TTTAGTTTCG
*
1588051 CGTTACGATTTTCATTTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
*
1588085 CGTTGCGATTTTCA-TTTCGCATTGTGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
1588118 CGTTGCGAT
1 CGTTGCGAT
1588127 AGTCTGTTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 27 0.68
34 13 0.32
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.46
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
Found at i:1589740 original size:42 final size:42
Alignment explanation
Indices: 1589634--1589744 Score: 111
Period size: 42 Copynumber: 2.7 Consensus size: 42
1589624 TCTAAAATGT
* * *
1589634 TGGGAG-GGACCTCTTCAACGAT-ACAGTGGCCTCTTGAACGG
1 TGGGAGAGG-CCTCTTGAACGATGACAGGGGCCTCTTGAACGA
* * ** *
1589675 TGGGAGGGGACTCTTGAGGGATGATAGGGGCCTCTTGAACGA
1 TGGGAGAGGCCTCTTGAACGATGACAGGGGCCTCTTGAACGA
1589717 TAGGG-GAGGCCTCTTGAACGATGACAGG
1 T-GGGAGAGGCCTCTTGAACGATGACAGG
1589745 TGAGTCGGGC
Statistics
Matches: 55, Mismatches: 12, Indels: 5
0.76 0.17 0.07
Matches are distributed among these distances:
41 15 0.27
42 37 0.67
43 3 0.05
ACGTcount: A:0.23, C:0.19, G:0.38, T:0.21
Consensus pattern (42 bp):
TGGGAGAGGCCTCTTGAACGATGACAGGGGCCTCTTGAACGA
Found at i:1590250 original size:20 final size:20
Alignment explanation
Indices: 1590225--1590290 Score: 69
Period size: 20 Copynumber: 3.3 Consensus size: 20
1590215 ACTTAAAATT
1590225 GCAACGCGAAAATGACTATC
1 GCAACGCGAAAATGACTATC
* * *
1590245 GTAACGCTATAATGACTATC
1 GCAACGCGAAAATGACTATC
* **
1590265 GCAATGCGAATTTGACTATC
1 GCAACGCGAAAATGACTATC
*
1590285 ACAACG
1 GCAACG
1590291 AGAGAATCGC
Statistics
Matches: 35, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.23
Consensus pattern (20 bp):
GCAACGCGAAAATGACTATC
Found at i:1590358 original size:20 final size:20
Alignment explanation
Indices: 1590333--1590571 Score: 247
Period size: 20 Copynumber: 12.6 Consensus size: 20
1590323 GCGATTCTTT
**
1590333 CATTGCGATAGTCAAATTCG
1 CATTGCGATAGTCATTTTCG
*
1590353 CATTGCGATAGTCAAATTT-G
1 CATTGCGATAGTC-ATTTTCG
*
1590373 CATTGTGATAGTCATTTTCG
1 CATTGCGATAGTCATTTTCG
1590393 CATTGCGATAGTCATTTTCG
1 CATTGCGATAGTCATTTTCG
*
1590413 CGTTGCGAT--T--TTGTT-G
1 CATTGCGATAGTCATT-TTCG
**
1590429 --TTGCGATTTTCA-TTTCG
1 CATTGCGATAGTCATTTTCG
*
1590446 CATTGCGAT--TC--TCTCG
1 CATTGCGATAGTCATTTTCG
1590462 --TTGCGATAGTCATTTTCG
1 CATTGCGATAGTCATTTTCG
* *
1590480 CGTTGCGATAGTCATTTTCA
1 CATTGCGATAGTCATTTTCG
*
1590500 CGTTGCGATAGTCATTTTCG
1 CATTGCGATAGTCATTTTCG
1590520 CATTGCGATAGTCATTTTCG
1 CATTGCGATAGTCATTTTCG
*
1590540 TATTGCGATAGTCATTTTCG
1 CATTGCGATAGTCATTTTCG
1590560 CATTGCGATAGT
1 CATTGCGATAGT
1590572 AAACTATTCT
Statistics
Matches: 191, Mismatches: 12, Indels: 32
0.81 0.05 0.14
Matches are distributed among these distances:
14 14 0.07
16 12 0.06
17 6 0.03
18 5 0.03
19 11 0.06
20 139 0.73
21 4 0.02
ACGTcount: A:0.19, C:0.18, G:0.21, T:0.41
Consensus pattern (20 bp):
CATTGCGATAGTCATTTTCG
Found at i:1590489 original size:127 final size:126
Alignment explanation
Indices: 1590303--1590548 Score: 368
Period size: 127 Copynumber: 1.9 Consensus size: 126
1590293 AGAATCGCAA
* *
1590303 TGCGATTTTCATTTTGCATTGCGATTCTTTCATTGCGATAGTCAAATTCGCATTGCGATAGTCAA
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCATTGCGATAGTCAAATTCGCATTGCGATAGTC--
* *
1590368 ATTTGCA-TTGTGATAGTCATTTTCGCATTGCGATAGTCATTTTCGCGTTGCGATTTTGTTGT
64 ATTTGCACTTGCGATAGTCATTTTCGCATTGCGATAGTCATTTTCGCATTGCGATTTTGTTGT
* ** *
1590430 TGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATAGTCATTTTCGCGTTGCGATAGTCAT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCATTGCGATAGTCAAATTCGCATTGCGATAGTCAT
* *
1590495 TTTCACGTTGCGATAGTCATTTTCGCATTGCGATAGTCATTTTCGTATTGCGAT
66 TTGCAC-TTGCGATAGTCATTTTCGCATTGCGATAGTCATTTTCGCATTGCGAT
1590549 AGTCATTTTC
Statistics
Matches: 107, Mismatches: 10, Indels: 4
0.88 0.08 0.03
Matches are distributed among these distances:
125 6 0.06
127 101 0.94
ACGTcount: A:0.18, C:0.18, G:0.21, T:0.43
Consensus pattern (126 bp):
TGCGATTTTCATTTCGCATTGCGATTCTCTCATTGCGATAGTCAAATTCGCATTGCGATAGTCAT
TTGCACTTGCGATAGTCATTTTCGCATTGCGATAGTCATTTTCGCATTGCGATTTTGTTGT
Found at i:1592470 original size:20 final size:20
Alignment explanation
Indices: 1592447--1592496 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
1592437 TTGAAACTTT
1592447 AAATCGCAACACGAAAATGA
1 AAATCGCAACACGAAAATGA
1592467 AAATCGCAACACGAAAATGA
1 AAATCGCAACACGAAAATGA
**
1592487 CTATCGCAAC
1 AAATCGCAAC
1592497 GCAAGAATCG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.50, C:0.24, G:0.14, T:0.12
Consensus pattern (20 bp):
AAATCGCAACACGAAAATGA
Found at i:1592526 original size:33 final size:34
Alignment explanation
Indices: 1592468--1592541 Score: 98
Period size: 33 Copynumber: 2.2 Consensus size: 34
1592458 CGAAAATGAA
**
1592468 AATCGCAACACGAAAATGACTATCGCAACG-CAAG
1 AATCGCAACACGAAAATGAAAATCGCAACGAC-AG
*
1592502 AATCGCAACGCG-AAATGAAAATCGCAACGACAG
1 AATCGCAACACGAAAATGAAAATCGCAACGACAG
1592535 AATCGCA
1 AATCGCA
1592542 TTGCGATAGT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
33 24 0.67
34 12 0.33
ACGTcount: A:0.45, C:0.26, G:0.19, T:0.11
Consensus pattern (34 bp):
AATCGCAACACGAAAATGAAAATCGCAACGACAG
Found at i:1592893 original size:22 final size:22
Alignment explanation
Indices: 1592866--1592908 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1592856 TGACCGTGAA
*
1592866 TGATTTCGCCGGAGATGGGGAC
1 TGATTTCGCCGGAGATAGGGAC
*
1592888 TGATTTCGTCGGAGATAGGGA
1 TGATTTCGCCGGAGATAGGGA
1592909 TGGATGTCGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.21, C:0.14, G:0.40, T:0.26
Consensus pattern (22 bp):
TGATTTCGCCGGAGATAGGGAC
Found at i:1593130 original size:20 final size:20
Alignment explanation
Indices: 1593106--1593238 Score: 205
Period size: 20 Copynumber: 6.7 Consensus size: 20
1593096 CGATAGTCAG
* *
1593106 ATTCGCGTTGCGATTTACAT
1 ATTCGCATTGCGATTTACGT
* *
1593126 TTTCGCATTGCGATTT-CATT
1 ATTCGCATTGCGATTTAC-GT
1593146 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
1593166 ATTCGCATTGTGATTTACGT
1 ATTCGCATTGCGATTTACGT
1593186 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
1593206 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
1593226 ATTCGCATTGCGA
1 ATTCGCATTGCGA
1593239 ATTTGGAAAA
Statistics
Matches: 104, Mismatches: 7, Indels: 4
0.90 0.06 0.03
Matches are distributed among these distances:
19 1 0.01
20 102 0.98
21 1 0.01
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.41
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:1593252 original size:21 final size:21
Alignment explanation
Indices: 1593228--1593280 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
1593218 ATTTACGTAT
*
1593228 TCGCATTGCGAATTTGGAAAA
1 TCGCAATGCGAATTTGGAAAA
*
1593249 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAATTTGGAAAA
*
1593270 TTGCAATGCGA
1 TCGCAATGCGA
1593281 TAGTCAGAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.25
Consensus pattern (21 bp):
TCGCAATGCGAATTTGGAAAA
Found at i:1593769 original size:21 final size:21
Alignment explanation
Indices: 1593736--1593788 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
1593726 ATTCTGACTA
1593736 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* * *
1593757 TCGCGTTGTGATTTTCCTAAT
1 TCGCATTGCGATTTTCCAAAT
*
1593778 TCGCAATGCGA
1 TCGCATTGCGA
1593789 ATACGTAAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:1593803 original size:20 final size:20
Alignment explanation
Indices: 1593778--1593815 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1593768 TTTTCCTAAT
1593778 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
1593798 TCGCAATGCGATTACGTA
1 TCGCAATGCGAATACGTA
1593816 TTGCGATTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:1593822 original size:13 final size:13
Alignment explanation
Indices: 1593804--1593830 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1593794 TAAATCGCAA
1593804 TGCGATTACGTAT
1 TGCGATTACGTAT
1593817 TGCGATTACGTAT
1 TGCGATTACGTAT
1593830 T
1 T
1593831 CGCATTGCGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.15, G:0.22, T:0.41
Consensus pattern (13 bp):
TGCGATTACGTAT
Found at i:1593827 original size:33 final size:33
Alignment explanation
Indices: 1593784--1593848 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
1593774 TAATTCGCAA
1593784 TGCGAATACGTAAATCGCAATGCGA-TTACGTAT
1 TGCGAATACGT-AATCGCAATGCGATTTACGTAT
* * *
1593817 TGCGATTACGTATTCGCATTGCGATTTACGTA
1 TGCGAATACGTAATCGCAATGCGATTTACGTA
1593849 ATCGCATTGC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 11 0.39
33 17 0.61
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.32
Consensus pattern (33 bp):
TGCGAATACGTAATCGCAATGCGATTTACGTAT
Found at i:1593847 original size:20 final size:20
Alignment explanation
Indices: 1593815--1593956 Score: 146
Period size: 20 Copynumber: 7.0 Consensus size: 20
1593805 GCGATTACGT
*
1593815 ATTGCGA-TTACGTATTCGC
1 ATTGCGATTTACGTAATCGC
1593834 ATTGCGATTTACGTAATCGC
1 ATTGCGATTTACGTAATCGC
1593854 ATTGCGATTTACGTAATCGC
1 ATTGCGATTTACGTAATCGC
* * *
1593874 AATGCGATTTTCCTAATTCGC
1 ATTGCGATTTACGTAA-TCGC
* ** *
1593895 ATTGCGATTTTCCCAATTCAC
1 ATTGCGATTTACGTAA-TCGC
1593916 ACTT-CGATTTACGTAATCGC
1 A-TTGCGATTTACGTAATCGC
*
1593936 ATTTCGATTTA-GTAAATCGC
1 ATTGCGATTTACGT-AATCGC
1593956 A
1 A
1593957 ACGAGATTCT
Statistics
Matches: 107, Mismatches: 11, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
19 11 0.10
20 62 0.58
21 32 0.30
22 2 0.02
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37
Consensus pattern (20 bp):
ATTGCGATTTACGTAATCGC
Found at i:1593936 original size:41 final size:40
Alignment explanation
Indices: 1593836--1593946 Score: 123
Period size: 41 Copynumber: 2.7 Consensus size: 40
1593826 GTATTCGCAT
** *
1593836 TGCGATTTACGTAATCGCATTGCGATTTACGTAATCGCAA
1 TGCGATTTACGTAATCGCATTGCGATTTACCCAATCACAA
* * * *
1593876 TGCGATTTTCCTAATTCGCATTGCGATTTTCCCAATTCACAC
1 TGCGATTTACGTAA-TCGCATTGCGATTTACCCAA-TCACAA
* *
1593918 TTCGATTTACGTAATCGCATTTCGATTTA
1 TGCGATTTACGTAATCGCATTGCGATTTA
1593947 GTAAATCGCA
Statistics
Matches: 57, Mismatches: 12, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
40 12 0.21
41 30 0.53
42 15 0.26
ACGTcount: A:0.24, C:0.23, G:0.15, T:0.38
Consensus pattern (40 bp):
TGCGATTTACGTAATCGCATTGCGATTTACCCAATCACAA
Found at i:1594841 original size:24 final size:24
Alignment explanation
Indices: 1594814--1594867 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1594804 GTATTCGAAA
1594814 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
1594838 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
1594862 TTTGAT
1 TTTGAT
1594868 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Done.