Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 ID=Chr07-JGI_221_v2.0
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: 60982465
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 868082 characters in sequence are not A, C, G, or T
File 134 of 204
Found at i:40766896 original size:18 final size:19
Alignment explanation
Indices: 40766858--40766896 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
40766848 TTAAAATAAT
**
40766858 TTTTAAAATTTATTTTTAA
1 TTTTAAAATTTATAATTAA
40766877 TTTTAAAATTT-TAATTAA
1 TTTTAAAATTTATAATTAA
40766895 TT
1 TT
40766897 ATCGATATGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTTAAAATTTATAATTAA
Found at i:40767175 original size:7 final size:7
Alignment explanation
Indices: 40767148--40767177 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
40767138 ATCACCGAGA
*
40767148 ATATTAA
1 ATATTAT
40767155 ATATTAT
1 ATATTAT
40767162 ATATTAT
1 ATATTAT
40767169 ATATTAT
1 ATATTAT
40767176 AT
1 AT
40767178 TAATATTGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (7 bp):
ATATTAT
Found at i:40768085 original size:39 final size:39
Alignment explanation
Indices: 40767991--40768086 Score: 97
Period size: 39 Copynumber: 2.4 Consensus size: 39
40767981 TCACGAATCG
*
40767991 CCTCGTCACAACTTCGTC-CATCGTCATGACGTTAGGAAACT
1 CCTCGTCACAA---CGTCACATCATCATGACGTTAGGAAACT
****
40768032 CCTCGTTGTGACGTCACATCATCATGACGTT-GGAAACCT
1 CCTCGTCACAACGTCACATCATCATGACGTTAGGAAA-CT
40768071 CCTCGTCACAACGTCA
1 CCTCGTCACAACGTCA
40768087 TCGCCTGTTG
Statistics
Matches: 44, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
38 9 0.20
39 28 0.64
41 7 0.16
ACGTcount: A:0.24, C:0.32, G:0.18, T:0.26
Consensus pattern (39 bp):
CCTCGTCACAACGTCACATCATCATGACGTTAGGAAACT
Found at i:40769625 original size:35 final size:35
Alignment explanation
Indices: 40769581--40769649 Score: 120
Period size: 35 Copynumber: 2.0 Consensus size: 35
40769571 TTCAATTTTG
*
40769581 GAAAGTGATAATTTATCATTCAATAGATACATTTA
1 GAAACTGATAATTTATCATTCAATAGATACATTTA
*
40769616 GAAACTGATAATTTATCATTCAATGGATACATTT
1 GAAACTGATAATTTATCATTCAATAGATACATTT
40769650 TCATGGGACA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.41, C:0.10, G:0.12, T:0.38
Consensus pattern (35 bp):
GAAACTGATAATTTATCATTCAATAGATACATTTA
Found at i:40772028 original size:34 final size:34
Alignment explanation
Indices: 40771964--40772056 Score: 96
Period size: 34 Copynumber: 2.7 Consensus size: 34
40771954 ATCAGTTGTT
* * **
40771964 CATTGATGTGCCCGAATAGCCTTGTTGATATGCC
1 CATTGATGTGCACGAACAGCCTTGAAGATATGCC
* *
40771998 CATTGATGTGTACGAACAGCCTTGAAGATATGTC
1 CATTGATGTGCACGAACAGCCTTGAAGATATGCC
** * *
40772032 TTTTGATGTGCACGAGCAGCTTTGA
1 CATTGATGTGCACGAACAGCCTTGA
40772057 TAGTTGCCTT
Statistics
Matches: 48, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
34 48 1.00
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.32
Consensus pattern (34 bp):
CATTGATGTGCACGAACAGCCTTGAAGATATGCC
Found at i:40781594 original size:61 final size:63
Alignment explanation
Indices: 40781518--40781640 Score: 171
Period size: 62 Copynumber: 2.0 Consensus size: 63
40781508 TAAAAAAGTT
*
40781518 TAATAATAAAAAATTTAATCATA-TTTTAATATAATTATTATTA-AATATAGTT-TAATAAAAA
1 TAATAATAAAAAATTTAATAATATTTTTAATATAATTATTATTATAATATA-TTATAATAAAAA
* * * *
40781579 TAATAATATATAATTTAATAATATTTTTAATATAATTATTTTTATATTATATTATAATAAAA
1 TAATAATAAAAAATTTAATAATATTTTTAATATAATTATTATTATAATATATTATAATAAAA
40781641 TATTTTATTT
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
61 20 0.37
62 21 0.39
63 13 0.24
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (63 bp):
TAATAATAAAAAATTTAATAATATTTTTAATATAATTATTATTATAATATATTATAATAAAAA
Found at i:40781638 original size:25 final size:25
Alignment explanation
Indices: 40781610--40781687 Score: 61
Period size: 30 Copynumber: 3.0 Consensus size: 25
40781600 TATTTTTAAT
40781610 ATAATTATTTTTATATTATATTATA
1 ATAATTATTTTTATATTATATTATA
* *
40781635 ATAAAATATTTTATTTTAAATTATATTA-A
1 AT---A-ATTAT-TTTTATATTATATTATA
* *
40781664 A-AATTAGTTTTATATTAAATTATA
1 ATAATTATTTTTATATTATATTATA
40781688 TTAAAATATT
Statistics
Matches: 41, Mismatches: 6, Indels: 13
0.68 0.10 0.22
Matches are distributed among these distances:
23 13 0.32
24 4 0.10
25 3 0.07
28 1 0.02
29 6 0.15
30 14 0.34
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (25 bp):
ATAATTATTTTTATATTATATTATA
Found at i:40781682 original size:28 final size:27
Alignment explanation
Indices: 40781612--40781693 Score: 105
Period size: 28 Copynumber: 3.0 Consensus size: 27
40781602 TTTTTAATAT
* *
40781612 AATTATTTTTATATTATATTATAAT-AA
1 AATTA-TTTTATATTAAATTATATTAAA
*
40781639 AA-TATTTTATTTTAAATTATATTAAA
1 AATTATTTTATATTAAATTATATTAAA
40781665 AATTAGTTTTATATTAAATTATATTAAA
1 AATTA-TTTTATATTAAATTATATTAAA
40781693 A
1 A
40781694 TATTTCAAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
25 16 0.33
26 6 0.12
27 4 0.08
28 22 0.46
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.52
Consensus pattern (27 bp):
AATTATTTTATATTAAATTATATTAAA
Found at i:40794140 original size:15 final size:14
Alignment explanation
Indices: 40794120--40794181 Score: 61
Period size: 14 Copynumber: 4.2 Consensus size: 14
40794110 TTTTTATACT
*
40794120 TTAATTTAAGCTTAA
1 TTAA-TTAAACTTAA
*
40794135 TTAATTAAAATTAA
1 TTAATTAAACTTAA
40794149 TTAATTAAACTTAAA
1 TTAATTAAACTT-AA
* *
40794164 TTAACTAAGCCTTAA
1 TTAATTAA-ACTTAA
40794179 TTA
1 TTA
40794182 GTAATTAATA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
14 19 0.47
15 18 0.45
16 3 0.08
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.42
Consensus pattern (14 bp):
TTAATTAAACTTAA
Found at i:40816937 original size:16 final size:15
Alignment explanation
Indices: 40816910--40816948 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
40816900 ATAGCTAGTA
*
40816910 TATAATTATATTTAT
1 TATAATTATATTAAT
40816925 TATAATATATATTAAT
1 TATAAT-TATATTAAT
*
40816941 TATTATTA
1 TATAATTA
40816949 ACTTTGCCTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TATAATTATATTAAT
Found at i:40818469 original size:3 final size:3
Alignment explanation
Indices: 40818461--40818497 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
40818451 GAGGATCTCA
* *
40818461 AAG AAG AAG AAG AAA AAG AAG AAG AAG AAT AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
40818498 TCCCACAAAG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.70, C:0.00, G:0.27, T:0.03
Consensus pattern (3 bp):
AAG
Found at i:40818480 original size:15 final size:15
Alignment explanation
Indices: 40818460--40818497 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
40818450 TGAGGATCTC
40818460 AAAGAAGAAGAAGAA
1 AAAGAAGAAGAAGAA
40818475 AAAGAAGAAGAAGAA
1 AAAGAAGAAGAAGAA
*
40818490 TAAGAAGA
1 AAAGAAGA
40818498 TCCCACAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.71, C:0.00, G:0.26, T:0.03
Consensus pattern (15 bp):
AAAGAAGAAGAAGAA
Found at i:40819777 original size:17 final size:18
Alignment explanation
Indices: 40819738--40819781 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
40819728 AAAAAGAAAA
40819738 AAAAGAGAACATATGTACTC
1 AAAAGA-AACATATGTAC-C
*
40819758 AAAAGAAATATATGTA-C
1 AAAAGAAACATATGTACC
40819775 AAAAGAA
1 AAAAGAA
40819782 CATGTGAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 8 0.35
19 9 0.39
20 6 0.26
ACGTcount: A:0.59, C:0.09, G:0.14, T:0.18
Consensus pattern (18 bp):
AAAAGAAACATATGTACC
Found at i:40824344 original size:72 final size:72
Alignment explanation
Indices: 40824227--40824368 Score: 248
Period size: 72 Copynumber: 2.0 Consensus size: 72
40824217 TCTCGGATTT
* *
40824227 AAAAAAGGGATCATGCCCAGTAAGTTAGGACACGATCTTTTCTTAATTCCCGAGATCGTTTAAAA
1 AAAAAAAGGATCATGCCCAGTAAGTTAGGACACGATCTCTTCTTAATTCCCGAGATCGTTTAAAA
40824292 CTTGAGA
66 CTTGAGA
**
40824299 AAAAAAAGGATCATGCCCAGTAAGTTAGGACACGATCTCTTCTTAATTCTTGAGATCGTTTAAAA
1 AAAAAAAGGATCATGCCCAGTAAGTTAGGACACGATCTCTTCTTAATTCCCGAGATCGTTTAAAA
40824364 CTTGA
66 CTTGA
40824369 ATTGGACAAG
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
72 66 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (72 bp):
AAAAAAAGGATCATGCCCAGTAAGTTAGGACACGATCTCTTCTTAATTCCCGAGATCGTTTAAAA
CTTGAGA
Found at i:40824709 original size:4 final size:4
Alignment explanation
Indices: 40824700--40824727 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
40824690 AATGAAAATG
40824700 TAAA TAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA
40824728 ATGAATAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
TAAA
Found at i:40824734 original size:9 final size:9
Alignment explanation
Indices: 40824701--40824738 Score: 53
Period size: 8 Copynumber: 4.4 Consensus size: 9
40824691 ATGAAAATGT
40824701 AAATAAAT-
1 AAATAAATA
40824709 AAATAAAT-
1 AAATAAATA
40824717 AAATAAATA
1 AAATAAATA
*
40824726 AAATGAATA
1 AAATAAATA
40824735 AAAT
1 AAAT
40824739 TATAAAAAGG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
8 16 0.57
9 12 0.43
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (9 bp):
AAATAAATA
Found at i:40825122 original size:17 final size:17
Alignment explanation
Indices: 40825098--40825132 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
40825088 TTTTTTAATT
40825098 TAATATTACA-TTTACA
1 TAATATTACATTTTACA
40825114 TAATAATTACATTTTACA
1 TAAT-ATTACATTTTACA
40825132 T
1 T
40825133 TTCTCCCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.24
17 6 0.35
18 7 0.41
ACGTcount: A:0.43, C:0.11, G:0.00, T:0.46
Consensus pattern (17 bp):
TAATATTACATTTTACA
Found at i:40829285 original size:18 final size:18
Alignment explanation
Indices: 40829262--40829297 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
40829252 TGGTTGCAAA
40829262 AAGGACGATGAGGACGAT
1 AAGGACGATGAGGACGAT
40829280 AAGGACGATGAGGACGAT
1 AAGGACGATGAGGACGAT
40829298 GACGATGATG
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:0.39, C:0.11, G:0.39, T:0.11
Consensus pattern (18 bp):
AAGGACGATGAGGACGAT
Found at i:40829307 original size:18 final size:18
Alignment explanation
Indices: 40829265--40829308 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
40829255 TTGCAAAAAG
*
40829265 GACGATGAGGACGATAAG
1 GACGATGAGGACGATAAC
*
40829283 GACGATGAGGACGATGAC
1 GACGATGAGGACGATAAC
*
40829301 GATGATGA
1 GACGATGA
40829309 TGTTTCTTCG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.36, C:0.11, G:0.39, T:0.14
Consensus pattern (18 bp):
GACGATGAGGACGATAAC
Found at i:40829308 original size:9 final size:9
Alignment explanation
Indices: 40829263--40829299 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
40829253 GGTTGCAAAA
40829263 AGGACGATG
1 AGGACGATG
*
40829272 AGGACGATA
1 AGGACGATG
40829281 AGGACGATG
1 AGGACGATG
40829290 AGGACGATG
1 AGGACGATG
40829299 A
1 A
40829300 CGATGATGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.38, C:0.11, G:0.41, T:0.11
Consensus pattern (9 bp):
AGGACGATG
Found at i:40829547 original size:30 final size:30
Alignment explanation
Indices: 40829511--40829569 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
40829501 AAAGATAGGT
40829511 TGAAGCAAAATTACAGATTGGGATTTTCAG
1 TGAAGCAAAATTACAGATTGGGATTTTCAG
40829541 TGAAGCAAAATTACAGATTGGGATTTTCA
1 TGAAGCAAAATTACAGATTGGGATTTTCA
40829570 ATGCTTGATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.37, C:0.10, G:0.22, T:0.31
Consensus pattern (30 bp):
TGAAGCAAAATTACAGATTGGGATTTTCAG
Found at i:40830641 original size:18 final size:18
Alignment explanation
Indices: 40830605--40830667 Score: 65
Period size: 18 Copynumber: 3.6 Consensus size: 18
40830595 AGTATATATA
* *
40830605 AATAAAAAT-ATAATGAT
1 AATAAAAATAATACTAAT
* *
40830622 AATAACAATAATATTAAT
1 AATAAAAATAATACTAAT
* *
40830640 AATAATAATACTACTAAT
1 AATAAAAATAATACTAAT
40830658 AATAAAAATA
1 AATAAAAATA
40830668 TAATTTATTA
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
17 8 0.21
18 30 0.79
ACGTcount: A:0.63, C:0.05, G:0.02, T:0.30
Consensus pattern (18 bp):
AATAAAAATAATACTAAT
Found at i:40830690 original size:3 final size:3
Alignment explanation
Indices: 40830605--40830671 Score: 57
Period size: 3 Copynumber: 23.0 Consensus size: 3
40830595 AGTATATATA
* * * * *
40830605 AAT AAA AAT -AT AAT GAT AAT AAC AAT AAT ATT AAT AAT AAT AAT ACT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
40830652 ACT AAT AAT AAA AAT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT
40830672 TTATTATTTT
Statistics
Matches: 50, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
2 4 0.08
3 46 0.92
ACGTcount: A:0.63, C:0.04, G:0.01, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:40832428 original size:89 final size:89
Alignment explanation
Indices: 40832277--40832688 Score: 517
Period size: 89 Copynumber: 4.6 Consensus size: 89
40832267 CTGCAAGCTA
** *
40832277 TGGTGTCTTCGATCTGCTTCGTTGTCAGTACAGGAAGGCAAGATCTACTATCTTCAGTCTGCTCC
1 TGGTGTCTTCGATCTGCTTCGTTGTCAGTACAGGAAAACAAGATCTGCTATCTTCAGTCTGCTCC
* *
40832342 GCTG-CA-AACCCAGGGAGGCAAGAC
66 GCTGTCAGAA--CAGGAAGGCAAGGC
* * * * *
40832366 TGGTGTCTTCGATCTGCTTCGCTATCAGTACGGGAAAACGAGATCTGTTATCTTCAGTCTGCTCC
1 TGGTGTCTTCGATCTGCTTCGTTGTCAGTACAGGAAAACAAGATCTGCTATCTTCAGTCTGCTCC
*
40832431 GCTGTCAGTACAGGAAGGCAAGGC
66 GCTGTCAGAACAGGAAGGCAAGGC
* * **
40832455 TGGTGTCTTCAATCTGCTTCGTTGTCAATACAGGAAGGCAAGATCTGCTATCTTCAGTCTGCTCC
1 TGGTGTCTTCGATCTGCTTCGTTGTCAGTACAGGAAAACAAGATCTGCTATCTTCAGTCTGCTCC
* *
40832520 GCTGTCAGTACAGGAAGACAAGGC
66 GCTGTCAGAACAGGAAGGCAAGGC
* * *
40832544 TAGTGTCTTCGATCTGCTTCATTGTCAGTACAGGAAGGA-AAGATCTGCTATCTTCAGTCTGCTC
1 TGGTGTCTTCGATCTGCTTCGTTGTCAGTACAGGAA-AACAAGATCTGCTATCTTCAGTCTGCTC
* *
40832608 CGCTGTCA-ACACAGGATGGTAAGGC
65 CGCTGTCAGA-ACAGGAAGGCAAGGC
* * ** *
40832633 TGGTGTCTTCGATCTGCTTCGCTGTCAGTGCAGGAAGGCAAGATCTACTATCTTCA
1 TGGTGTCTTCGATCTGCTTCGTTGTCAGTACAGGAAAACAAGATCTGCTATCTTCA
40832689 CTGATCTGTT
Statistics
Matches: 282, Mismatches: 36, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
88 1 0.00
89 277 0.98
90 3 0.01
91 1 0.00
ACGTcount: A:0.22, C:0.24, G:0.25, T:0.28
Consensus pattern (89 bp):
TGGTGTCTTCGATCTGCTTCGTTGTCAGTACAGGAAAACAAGATCTGCTATCTTCAGTCTGCTCC
GCTGTCAGAACAGGAAGGCAAGGC
Found at i:40832590 original size:178 final size:176
Alignment explanation
Indices: 40832277--40832688 Score: 585
Period size: 178 Copynumber: 2.3 Consensus size: 176
40832267 CTGCAAGCTA
40832277 TGGTGTCTTCGATCTGCTTCGTTGTCAGTACAGGAAGGCAAGATCTACTATCTTCAGTCTGCTCC
1 TGGTGTCTTCGATCTGCTTCGTTGTCAGTACAGGAAGGCAAGATCTACTATCTTCAGTCTGCTCC
* * * * *
40832342 GCTGCAAACCCAGGGAGGCAAGACTGGTGTCTTCGATCTGCTTCGCTATCAGTACGGGAAAACGA
66 GCTGCAAA-CCAGGAAGACAAGACTAGTGTCTTCGATCTGCTTCACTATCAGTACAGGAAAAC-A
* **
40832407 GATCTGTTATCTTCAGTCTGCTCCGCTGTCAGTACAGGAAGGCAAGGC
129 GATCTGCTATCTTCAGTCTGCTCCGCTGTCAACACAGGAAGGCAAGGC
* * *
40832455 TGGTGTCTTCAATCTGCTTCGTTGTCAATACAGGAAGGCAAGATCTGCTATCTTCAGTCTGCTCC
1 TGGTGTCTTCGATCTGCTTCGTTGTCAGTACAGGAAGGCAAGATCTACTATCTTCAGTCTGCTCC
* * * *
40832520 GCTGTCAGTA-CAGGAAGACAAGGCTAGTGTCTTCGATCTGCTTCATTGTCAGTACAGGAAGGAA
66 GCTG-CA-AACCAGGAAGACAAGACTAGTGTCTTCGATCTGCTTCACTATCAGTACAGGAA--AA
* *
40832584 -AGATCTGCTATCTTCAGTCTGCTCCGCTGTCAACACAGGATGGTAAGGC
127 CAGATCTGCTATCTTCAGTCTGCTCCGCTGTCAACACAGGAAGGCAAGGC
* *
40832633 TGGTGTCTTCGATCTGCTTCGCTGTCAGTGCAGGAAGGCAAGATCTACTATCTTCA
1 TGGTGTCTTCGATCTGCTTCGTTGTCAGTACAGGAAGGCAAGATCTACTATCTTCA
40832689 CTGATCTGTT
Statistics
Matches: 208, Mismatches: 22, Indels: 8
0.87 0.09 0.03
Matches are distributed among these distances:
178 203 0.98
179 2 0.01
180 3 0.01
ACGTcount: A:0.22, C:0.24, G:0.25, T:0.28
Consensus pattern (176 bp):
TGGTGTCTTCGATCTGCTTCGTTGTCAGTACAGGAAGGCAAGATCTACTATCTTCAGTCTGCTCC
GCTGCAAACCAGGAAGACAAGACTAGTGTCTTCGATCTGCTTCACTATCAGTACAGGAAAACAGA
TCTGCTATCTTCAGTCTGCTCCGCTGTCAACACAGGAAGGCAAGGC
Found at i:40839792 original size:73 final size:73
Alignment explanation
Indices: 40839673--40839808 Score: 263
Period size: 73 Copynumber: 1.9 Consensus size: 73
40839663 TTTAAAAAAG
*
40839673 GGATCATGCCCAGTAAGTTAGGACACGATCTTTTCTTAATTCCCGAGATCGTTTAAAACTTGAGA
1 GGATCATGCCCAGTAAGTTAGGACACGATCTCTTCTTAATTCCCGAGATCGTTTAAAACTTGAGA
40839738 AAAACAAA
66 AAAACAAA
40839746 GGATCATGCCCAGTAAGTTAGGACACGATCTCTTCTTAATTCCCGAGATCGTTTAAAACTTGA
1 GGATCATGCCCAGTAAGTTAGGACACGATCTCTTCTTAATTCCCGAGATCGTTTAAAACTTGA
40839809 ATTGGAAAAG
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
73 62 1.00
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (73 bp):
GGATCATGCCCAGTAAGTTAGGACACGATCTCTTCTTAATTCCCGAGATCGTTTAAAACTTGAGA
AAAACAAA
Found at i:40840630 original size:3 final size:3
Alignment explanation
Indices: 40840624--40840661 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
40840614 ATAATATTAA
40840624 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TA
1 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TA
40840662 ATAATAATAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.32, G:0.00, T:0.34
Consensus pattern (3 bp):
TAC
Found at i:40840666 original size:3 final size:3
Alignment explanation
Indices: 40840660--40840698 Score: 62
Period size: 3 Copynumber: 13.3 Consensus size: 3
40840650 CTACTACTAC
*
40840660 TAA TAA TAA TAA TAA TAA TAA TAA TAT TAA TAA T-A TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
40840699 TTATTATTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:40883106 original size:5 final size:5
Alignment explanation
Indices: 40883086--40883119 Score: 50
Period size: 5 Copynumber: 6.4 Consensus size: 5
40883076 TTTTCCCATC
40883086 TTCTT TCTCTTT TTCTT TTCTT TTCTT TTCTT TT
1 TTCTT T-TC-TT TTCTT TTCTT TTCTT TTCTT TT
40883120 TATGTTTCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
5 20 0.74
6 4 0.15
7 3 0.11
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (5 bp):
TTCTT
Found at i:40883127 original size:22 final size:22
Alignment explanation
Indices: 40883086--40883129 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
40883076 TTTTCCCATC
*
40883086 TTCTTTCTCTTTTTCTTTTCTT
1 TTCTTTCTCTTTTTATTTTCTT
40883108 TTCTTT-TCTTTTTATGTTTCTT
1 TTCTTTCTCTTTTTAT-TTTCTT
40883130 CTTTCTTCTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.02, C:0.18, G:0.02, T:0.77
Consensus pattern (22 bp):
TTCTTTCTCTTTTTATTTTCTT
Found at i:40883138 original size:22 final size:21
Alignment explanation
Indices: 40883084--40883138 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 21
40883074 CTTTTTCCCA
*
40883084 TCTTCTTTC-TCTTTTTCTTT
1 TCTTCTTTCTTCTTTTTATTT
*
40883104 TCTT-TTCTTTTCTTTTTATGTT
1 TCTTCTT-TCTTCTTTTTAT-TT
40883126 TCTTCTTTCTTCT
1 TCTTCTTTCTTCT
40883139 GAATTTTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
19 2 0.07
20 5 0.18
21 8 0.29
22 11 0.39
23 2 0.07
ACGTcount: A:0.02, C:0.22, G:0.02, T:0.75
Consensus pattern (21 bp):
TCTTCTTTCTTCTTTTTATTT
Found at i:40885087 original size:15 final size:16
Alignment explanation
Indices: 40885057--40885091 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
40885047 CCTATTACAA
40885057 TTAGGGAAGAAAATTT
1 TTAGGGAAGAAAATTT
*
40885073 TTAGGGAAGAAATTTT
1 TTAGGGAAGAAAATTT
40885089 TTA
1 TTA
40885092 CTAATTCCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.23, T:0.37
Consensus pattern (16 bp):
TTAGGGAAGAAAATTT
Found at i:40895886 original size:29 final size:29
Alignment explanation
Indices: 40895853--40895911 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
40895843 GGCCTAGACC
40895853 GTGTGTCACACATAGCCCAACACACGGCT
1 GTGTGTCACACATAGCCCAACACACGGCT
* * *
40895882 GTGTGTCACACATGGCCTACCACACGGCT
1 GTGTGTCACACATAGCCCAACACACGGCT
40895911 G
1 G
40895912 GGTGGCTTCG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.24, C:0.34, G:0.24, T:0.19
Consensus pattern (29 bp):
GTGTGTCACACATAGCCCAACACACGGCT
Found at i:40896936 original size:37 final size:38
Alignment explanation
Indices: 40896849--40896940 Score: 116
Period size: 37 Copynumber: 2.4 Consensus size: 38
40896839 ACCACTTTGA
* *
40896849 CCACCCTGCACACCACATATGAGCTATAACGAGCCCAT
1 CCACCCTGCACACCACATATGAACTATAAAGAGCCCAT
* *
40896887 CCACCCTGCACACCACATA-GAACTTTGAAAG-GCTCAT
1 CCACCCTGCACACCACATATGAACTAT-AAAGAGCCCAT
*
40896924 CCACCCTACACACCACA
1 CCACCCTGCACACCACA
40896941 ATGTGGAACT
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
37 26 0.54
38 22 0.46
ACGTcount: A:0.33, C:0.41, G:0.11, T:0.15
Consensus pattern (38 bp):
CCACCCTGCACACCACATATGAACTATAAAGAGCCCAT
Found at i:40898879 original size:13 final size:14
Alignment explanation
Indices: 40898863--40898895 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
40898853 AAATAAAATG
40898863 GGAAAAAC-CAGAA
1 GGAAAAACGCAGAA
40898876 GGAAAAACGTCAGAA
1 GGAAAAACG-CAGAA
40898891 GGAAA
1 GGAAA
40898896 TTGCAAGGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 8 0.44
15 10 0.56
ACGTcount: A:0.58, C:0.12, G:0.27, T:0.03
Consensus pattern (14 bp):
GGAAAAACGCAGAA
Found at i:40905098 original size:24 final size:23
Alignment explanation
Indices: 40905066--40905112 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
40905056 AATATAACTC
*
40905066 TTTTTAAGAAAATATAATAAAACA
1 TTTTGAAGAAAA-ATAATAAAACA
*
40905090 TTTTGAAGAATAATAATAAAACA
1 TTTTGAAGAAAAATAATAAAACA
40905113 CTTGATAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.57, C:0.04, G:0.06, T:0.32
Consensus pattern (23 bp):
TTTTGAAGAAAAATAATAAAACA
Found at i:40906116 original size:23 final size:21
Alignment explanation
Indices: 40906067--40906117 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
40906057 GGATTATAAC
*
40906067 TAATAATTCTAAATTAAATTA
1 TAATATTTCTAAATTAAATTA
*
40906088 TAAATATTTCTAAATGTCAATTA
1 T-AATATTTCTAAAT-TAAATTA
40906111 GTAATAT
1 -TAATAT
40906118 GGTAGGAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 1 0.04
22 12 0.48
23 11 0.44
24 1 0.04
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (21 bp):
TAATATTTCTAAATTAAATTA
Found at i:40914228 original size:34 final size:34
Alignment explanation
Indices: 40914184--40914251 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 34
40914174 GCACAGTTGA
* *
40914184 ACAGTCTTGGGCCTAAGCCCTTTTCAGTATCAGTG
1 ACAGTCTTGGGCCTAAGCCCATCTCAGTA-CAGTG
*
40914219 ACAGT-TTGGGCCTTAGCCCATCTCAGTACAGTG
1 ACAGTCTTGGGCCTAAGCCCATCTCAGTACAGTG
40914252 TCAAAAATGC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
33 5 0.17
34 20 0.67
35 5 0.17
ACGTcount: A:0.21, C:0.26, G:0.24, T:0.29
Consensus pattern (34 bp):
ACAGTCTTGGGCCTAAGCCCATCTCAGTACAGTG
Found at i:40915264 original size:39 final size:40
Alignment explanation
Indices: 40915186--40915264 Score: 133
Period size: 40 Copynumber: 2.0 Consensus size: 40
40915176 ACAATTTTCG
*
40915186 ATGATTTTTCCAAAGTCAGAACAGGGGAACCTGAACCCAT
1 ATGATTTTTCCAAAGTCAGAACAGGGGAACCCGAACCCAT
*
40915226 ATGATTTTTCCAAAGTCAGAATA-GGGAACCCGAACCCAT
1 ATGATTTTTCCAAAGTCAGAACAGGGGAACCCGAACCCAT
40915265 TTTGACCTTG
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
39 15 0.41
40 22 0.59
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (40 bp):
ATGATTTTTCCAAAGTCAGAACAGGGGAACCCGAACCCAT
Found at i:40917828 original size:29 final size:29
Alignment explanation
Indices: 40917796--40917864 Score: 70
Period size: 29 Copynumber: 2.4 Consensus size: 29
40917786 GTTTAATAGT
40917796 TTTATAATTTTTAATTATATTTT-AA-ATTG
1 TTTATAATTTTTAA-TA-ATTTTCAATATTG
* * * *
40917825 TTTACAATTTATAATAATTTTCAATTTTT
1 TTTATAATTTTTAATAATTTTCAATATTG
40917854 TTTATAATTTT
1 TTTATAATTTT
40917865 ATTACAATTT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
27 5 0.16
28 4 0.12
29 23 0.72
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.62
Consensus pattern (29 bp):
TTTATAATTTTTAATAATTTTCAATATTG
Found at i:40917880 original size:39 final size:39
Alignment explanation
Indices: 40917799--40917881 Score: 98
Period size: 39 Copynumber: 2.1 Consensus size: 39
40917789 TAATAGTTTT
* *
40917799 ATAATTTTTAATTATATTTTAAATTGTTTACAATTTATA
1 ATAATTTTCAATTATATTTTAAATTGTTTACAATTTACA
* *
40917838 ATAATTTTCAATT-TTTTTTATAATTTTATTACAATTT-CA
1 ATAATTTTCAATTATATTTTA-AATTGT-TTACAATTTACA
40917877 ATAAT
1 ATAAT
40917882 CTATTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
38 6 0.16
39 23 0.61
40 9 0.24
ACGTcount: A:0.37, C:0.05, G:0.01, T:0.57
Consensus pattern (39 bp):
ATAATTTTCAATTATATTTTAAATTGTTTACAATTTACA
Found at i:40923505 original size:20 final size:21
Alignment explanation
Indices: 40923454--40923509 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 21
40923444 TAATAAGATA
*
40923454 TTAATAATATTTTTATTTTTAT
1 TTAAT-ATATTTTTATTATTAT
* *
40923476 TTTACA-ATTTTTATTATT-T
1 TTAATATATTTTTATTATTAT
40923495 TTAATATATTTTTAT
1 TTAATATATTTTTAT
40923510 CTTTTTTATA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
19 5 0.18
20 19 0.68
21 1 0.04
22 3 0.11
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (21 bp):
TTAATATATTTTTATTATTAT
Found at i:40923515 original size:20 final size:19
Alignment explanation
Indices: 40923454--40923517 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 19
40923444 TAATAAGATA
40923454 TTAATAATATTTTTATTTTT
1 TTAAT-ATATTTTTATTTTT
* *
40923474 ATT-TTACAATTTTTATTATTT
1 -TTAATA-TATTTTTATT-TTT
40923495 TTAATATATTTTTATCTTTT
1 TTAATATATTTTTAT-TTTT
40923515 TTA
1 TTA
40923518 TATTTTATAA
Statistics
Matches: 35, Mismatches: 4, Indels: 9
0.73 0.08 0.19
Matches are distributed among these distances:
19 1 0.03
20 26 0.74
21 8 0.23
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (19 bp):
TTAATATATTTTTATTTTT
Found at i:40929709 original size:92 final size:96
Alignment explanation
Indices: 40929589--40929806 Score: 268
Period size: 92 Copynumber: 2.3 Consensus size: 96
40929579 AATTTAATTT
* * *
40929589 TTTTATAATTTTTTATGGTTTTTAATTAAATTCTAACAATTTTTTAAAATTAAT-TCTTTCTAAT
1 TTTTATAATATTTTATGGTTTTTAATTAAATTCTAACAATTTTTTAAAAATAATGT-TTTCTAAA
*
40929653 TTTTTATGG-TTTT-T-A-ATTTTTTTCTAAA
65 TTTGTATGGTTTTTATAATATTTTTTTCTAAA
* * * * *
40929681 TTTTCTAA-ATATTTATGGTTTTTAATTAATTTCTATCAGTTTTTTAAAAATCATGTTTTCTAAA
1 TTTTATAATAT-TTTATGGTTTTTAATTAAATTCTAACAATTTTTTAAAAATAATGTTTTCTAAA
40929745 TTTGTATGGTTTTTAATAAATTATTTTTTTCTAAA
65 TTTGTATGGTTTTT-AT-AA-TATTTTTTTCTAAA
40929780 TTTTATAATATTTTATGGTTTTTAATT
1 TTTTATAATATTTTATGGTTTTTAATT
40929807 TTTAATTAAA
Statistics
Matches: 106, Mismatches: 10, Indels: 13
0.82 0.08 0.10
Matches are distributed among these distances:
91 1 0.01
92 60 0.57
93 5 0.05
95 1 0.01
97 1 0.01
99 36 0.34
100 2 0.02
ACGTcount: A:0.29, C:0.05, G:0.06, T:0.60
Consensus pattern (96 bp):
TTTTATAATATTTTATGGTTTTTAATTAAATTCTAACAATTTTTTAAAAATAATGTTTTCTAAAT
TTGTATGGTTTTTATAATATTTTTTTCTAAA
Found at i:40929714 original size:37 final size:37
Alignment explanation
Indices: 40929645--40929715 Score: 106
Period size: 37 Copynumber: 1.9 Consensus size: 37
40929635 AAATTAATTC
* * **
40929645 TTTCTAATTTTTTATGGTTTTTAATTTTTTTCTAAAT
1 TTTCTAAATATTTATGGTTTTTAATTAATTTCTAAAT
40929682 TTTCTAAATATTTATGGTTTTTAATTAATTTCTA
1 TTTCTAAATATTTATGGTTTTTAATTAATTTCTA
40929716 TCAGTTTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 30 1.00
ACGTcount: A:0.25, C:0.06, G:0.06, T:0.63
Consensus pattern (37 bp):
TTTCTAAATATTTATGGTTTTTAATTAATTTCTAAAT
Found at i:40943000 original size:29 final size:29
Alignment explanation
Indices: 40942951--40943234 Score: 164
Period size: 29 Copynumber: 9.8 Consensus size: 29
40942941 GTGCTGAACA
* * *
40942951 ATGGTCATAACCGTCTCTTTTCATATTTG
1 ATGGTCGTAACCATCCCTTTTCATATTTG
* * * *
40942980 ATGGTCGAAACCATCCGTTTTCATTAATCG
1 ATGGTCGTAACCATCCCTTTTCA-TATTTG
* * *
40943010 ATGGTCGTTACCATCCCTTTTCGTAGTTG
1 ATGGTCGTAACCATCCCTTTTCATATTTG
* * * **
40943039 ATGGTTGTCACCATCCCTTTTCATAATCA
1 ATGGTCGTAACCATCCCTTTTCATATTTG
** * * *
40943068 ATATTCGAAACTATCCCTTTTCA-A-TCG
1 ATGGTCGTAACCATCCCTTTTCATATTTG
*** ** * *
40943095 ATAACCAAAACTATCGCTTTTCATATTTG
1 ATGGTCGTAACCATCCCTTTTCATATTTG
* *
40943124 ATGGTCGTCACCATCCCTTTTCAT-TGGTG
1 ATGGTCGTAACCATCCCTTTTCATAT-TTG
* *
40943153 ATGGTCGTCACCATCCCTTTTCAT-TGTTA
1 ATGGTCGTAACCATCCCTTTTCATAT-TTG
* * * *
40943182 ATGGTCGTCACCATCCCTTTTAATAATCG
1 ATGGTCGTAACCATCCCTTTTCATATTTG
* *
40943211 ATAGTCG-AAGCTATCCCTTTTCAT
1 ATGGTCGTAA-CCATCCCTTTTCAT
40943235 TGGTTGATGA
Statistics
Matches: 199, Mismatches: 50, Indels: 12
0.76 0.19 0.05
Matches are distributed among these distances:
27 21 0.11
28 4 0.02
29 151 0.76
30 23 0.12
ACGTcount: A:0.23, C:0.25, G:0.14, T:0.38
Consensus pattern (29 bp):
ATGGTCGTAACCATCCCTTTTCATATTTG
Found at i:40943226 original size:143 final size:144
Alignment explanation
Indices: 40942967--40943233 Score: 401
Period size: 143 Copynumber: 1.9 Consensus size: 144
40942957 ATAACCGTCT
* *
40942967 CTTTTCATATTTGATGGTCGAAACCATCCGTTTTCATTAATCGATGGTCGTTACCATCCCTTTTC
1 CTTTTCATATTTGATGGTCGAAACCATCCCTTTTCATTAATCGATGGTCGTCACCATCCCTTTTC
* * * * *
40943032 GTAGTTGATGGTTGTCACCATCCCTTTTCATAATCAATATTCGAAACTATCCCTTTTCAATCGAT
66 ATAGTTAATGGTCGTCACCATCCCTTTTAATAATCAATAGTCGAAACTATCCCTTTTCAATCGAT
40943097 AACCAAAACTATCG
131 AACCAAAACTATCG
** **
40943111 CTTTTCATATTTGATGGTCGTCACCATCCCTTTTCATTGGT-GATGGTCGTCACCATCCCTTTTC
1 CTTTTCATATTTGATGGTCGAAACCATCCCTTTTCATTAATCGATGGTCGTCACCATCCCTTTTC
* * *
40943175 ATTGTTAATGGTCGTCACCATCCCTTTTAATAATCGATAGTCGAAGCTATCCCTTTTCA
66 ATAGTTAATGGTCGTCACCATCCCTTTTAATAATCAATAGTCGAAACTATCCCTTTTCA
40943234 TTGGTTGATG
Statistics
Matches: 109, Mismatches: 14, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
143 73 0.67
144 36 0.33
ACGTcount: A:0.23, C:0.25, G:0.13, T:0.39
Consensus pattern (144 bp):
CTTTTCATATTTGATGGTCGAAACCATCCCTTTTCATTAATCGATGGTCGTCACCATCCCTTTTC
ATAGTTAATGGTCGTCACCATCCCTTTTAATAATCAATAGTCGAAACTATCCCTTTTCAATCGAT
AACCAAAACTATCG
Found at i:40948367 original size:39 final size:39
Alignment explanation
Indices: 40948322--40948521 Score: 224
Period size: 39 Copynumber: 5.1 Consensus size: 39
40948312 AATAGAAATA
* *
40948322 CGGTGATTATTCAGGTTATGTGCCTAGCAAGCTGTGTGC
1 CGGTGATTATTCAGGCTATGTGCCTAGCAGGCTGTGTGC
* * *
40948361 TGGTGATTATTC-GAGCTATGTGCCTAACAGGTTGTGTGC
1 CGGTGATTATTCAG-GCTATGTGCCTAGCAGGCTGTGTGC
* *
40948400 CGGTGATTATTCGGGCTATGTGCTTAGCAGGCTGTGTGC
1 CGGTGATTATTCAGGCTATGTGCCTAGCAGGCTGTGTGC
** * *
40948439 AAGTGATTATTCAGGCTTTGTGCCTAGTAGGCTGTGTGC
1 CGGTGATTATTCAGGCTATGTGCCTAGCAGGCTGTGTGC
* * * * *
40948478 CGATGGTTATTCGGGCTATGTGCC-AGGCAAGCTATGTGC
1 CGGTGATTATTCAGGCTATGTGCCTA-GCAGGCTGTGTGC
40948517 CGGTG
1 CGGTG
40948522 TATTGAAAAT
Statistics
Matches: 133, Mismatches: 25, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
38 2 0.02
39 130 0.98
40 1 0.01
ACGTcount: A:0.17, C:0.17, G:0.33, T:0.33
Consensus pattern (39 bp):
CGGTGATTATTCAGGCTATGTGCCTAGCAGGCTGTGTGC
Found at i:40954074 original size:14 final size:14
Alignment explanation
Indices: 40954055--40954084 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
40954045 AGCCCAGTGG
40954055 TTCAGTGATTAAGC
1 TTCAGTGATTAAGC
*
40954069 TTCAGTGGTTAAGC
1 TTCAGTGATTAAGC
40954083 TT
1 TT
40954085 TTATATACTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.23, C:0.13, G:0.23, T:0.40
Consensus pattern (14 bp):
TTCAGTGATTAAGC
Found at i:40954947 original size:96 final size:96
Alignment explanation
Indices: 40954774--40954948 Score: 210
Period size: 96 Copynumber: 1.8 Consensus size: 96
40954764 TGCACGACTG
* * * ** *
40954774 TGTGCCAGGCTGTGTGAGACACTGACTTGAGTCACACGATTATATGTAAGGCAGTGTGTTAGACC
1 TGTGCCAGGCCGTGTGAGACACTGACTTGAGCCACACGATCATATGTAAGGCAGTGTGACAAACC
*
40954839 GTGTAACTCACTAACTTGAGTTACTCGGTCA
66 GTGTAACGCACTAACTTGAGTTACTCGGTCA
* * *
40954870 TGTGCCAGGCCGTGTGAGGCACTGACTTGAGCCACAC-ATCCATGTGCT-AGGCCGTGTGACAAA
1 TGTGCCAGGCCGTGTGAGACACTGACTTGAGCCACACGAT-CATATG-TAAGGCAGTGTGACAAA
* *
40954933 CCGTGTGAGGCACTAA
64 CCGTGTAACGCACTAA
40954949 TATAAGCCAC
Statistics
Matches: 65, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
95 2 0.03
96 62 0.95
97 1 0.02
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (96 bp):
TGTGCCAGGCCGTGTGAGACACTGACTTGAGCCACACGATCATATGTAAGGCAGTGTGACAAACC
GTGTAACGCACTAACTTGAGTTACTCGGTCA
Found at i:40959835 original size:21 final size:20
Alignment explanation
Indices: 40959795--40959836 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
40959785 TCCGGCGTCG
40959795 ATTTTGTAAGTGTTCTAAAA
1 ATTTTGTAAGTGTTCTAAAA
*
40959815 ATTTTGATAAGT-TTTTAAAA
1 ATTTTG-TAAGTGTTCTAAAA
40959835 AT
1 AT
40959837 ATGAGTAGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.38, C:0.02, G:0.12, T:0.48
Consensus pattern (20 bp):
ATTTTGTAAGTGTTCTAAAA
Found at i:40960112 original size:12 final size:12
Alignment explanation
Indices: 40960095--40960127 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
40960085 AATGGGGTAC
40960095 TAGAGGCCGAGG
1 TAGAGGCCGAGG
40960107 TAGAGGCCGAGG
1 TAGAGGCCGAGG
40960119 TAGAGGCCG
1 TAGAGGCCG
40960128 TAGAGGGGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.24, C:0.18, G:0.48, T:0.09
Consensus pattern (12 bp):
TAGAGGCCGAGG
Found at i:40970055 original size:22 final size:22
Alignment explanation
Indices: 40970030--40970085 Score: 78
Period size: 22 Copynumber: 2.5 Consensus size: 22
40970020 TGCTTTAGCT
40970030 CTTACTGTTCTACACTTCGGTG
1 CTTACTGTTCTACACTTCGGTG
* *
40970052 CTTAGTGATT-TGCACTTCGGTG
1 CTTACTG-TTCTACACTTCGGTG
40970074 CTTACTGTTCTA
1 CTTACTGTTCTA
40970086 TTAGTGCACT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
21 2 0.07
22 24 0.86
23 2 0.07
ACGTcount: A:0.14, C:0.23, G:0.20, T:0.43
Consensus pattern (22 bp):
CTTACTGTTCTACACTTCGGTG
Found at i:40971002 original size:20 final size:21
Alignment explanation
Indices: 40970978--40971043 Score: 68
Period size: 20 Copynumber: 3.3 Consensus size: 21
40970968 GATACCAGAG
40970978 GTAAAGTATCGATACTTTAC-A
1 GTAAAGTATCGATACTTT-CGA
* *
40970999 -TAAACTATAGATAC-TTCGA
1 GTAAAGTATCGATACTTTCGA
*
40971018 GCAAAGTATCGATACTTT-GA
1 GTAAAGTATCGATACTTTCGA
40971038 GTAAAG
1 GTAAAG
40971044 AATTGGTACT
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
18 1 0.03
19 3 0.08
20 30 0.83
21 2 0.06
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.30
Consensus pattern (21 bp):
GTAAAGTATCGATACTTTCGA
Found at i:40972896 original size:2 final size:2
Alignment explanation
Indices: 40972889--40972935 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
40972879 TTCCATTATC
*
40972889 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
40972931 AT AT A
1 AT AT A
40972936 GCAAATTCGC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:40973473 original size:19 final size:19
Alignment explanation
Indices: 40973451--40973529 Score: 65
Period size: 19 Copynumber: 4.2 Consensus size: 19
40973441 TGCACAAAGC
40973451 GCATCCTAGCACATGAAAT
1 GCATCCTAGCACATGAAAT
** * *
40973470 GCATATTAGCGCA-CAAA-
1 GCATCCTAGCACATGAAAT
*
40973487 GCACATCCTAGC-CATGAAGT
1 G--CATCCTAGCACATGAAAT
*
40973507 GCATCCTGGCACATGAAAT
1 GCATCCTAGCACATGAAAT
40973526 GCAT
1 GCAT
40973530 AAAGCCGTAC
Statistics
Matches: 45, Mismatches: 10, Indels: 10
0.69 0.15 0.15
Matches are distributed among these distances:
17 1 0.02
18 13 0.29
19 30 0.67
20 1 0.02
ACGTcount: A:0.34, C:0.27, G:0.19, T:0.20
Consensus pattern (19 bp):
GCATCCTAGCACATGAAAT
Found at i:40973473 original size:38 final size:37
Alignment explanation
Indices: 40973431--40973510 Score: 115
Period size: 38 Copynumber: 2.1 Consensus size: 37
40973421 ACAGACATTG
* * *
40973431 TGCATATTGGTGCACAAAGCGCATCCTAGCACATGAAA
1 TGCATATTAGCGCACAAAGCACATCCTAGC-CATGAAA
*
40973469 TGCATATTAGCGCACAAAGCACATCCTAGCCATGAAG
1 TGCATATTAGCGCACAAAGCACATCCTAGCCATGAAA
40973506 TGCAT
1 TGCAT
40973511 CCTGGCACAT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
37 11 0.29
38 27 0.71
ACGTcount: A:0.34, C:0.25, G:0.20, T:0.21
Consensus pattern (37 bp):
TGCATATTAGCGCACAAAGCACATCCTAGCCATGAAA
Found at i:40973675 original size:24 final size:22
Alignment explanation
Indices: 40973623--40973676 Score: 54
Period size: 24 Copynumber: 2.3 Consensus size: 22
40973613 TTTCATTATA
* *
40973623 CAATTTAATTCATATATCATTT
1 CAATTCAATTCATATATCATGT
*
40973645 CACATTCAATTTCATATTCTCATGT
1 CA-ATTCAA-TTCATA-TATCATGT
40973670 CAATTCA
1 CAATTCA
40973677 TCATCAATTC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 2 0.08
23 5 0.19
24 11 0.42
25 8 0.31
ACGTcount: A:0.33, C:0.20, G:0.02, T:0.44
Consensus pattern (22 bp):
CAATTCAATTCATATATCATGT
Found at i:40976106 original size:28 final size:30
Alignment explanation
Indices: 40976054--40976129 Score: 79
Period size: 28 Copynumber: 2.6 Consensus size: 30
40976044 TAATTAATTT
*
40976054 AAAT-TATTTATAAAATTAATGATAC-ATA
1 AAATATATTTAAAAAATTAATGATACAATA
40976082 AAATAT-TTTAAAAAATTAAAT-ATACTAATA
1 AAATATATTTAAAAAATT-AATGATAC-AATA
* *
40976112 AATTATATTTAAATAATT
1 AAATATATTTAAAAAATT
40976130 TAACATAATA
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
28 18 0.45
29 4 0.10
30 8 0.20
31 10 0.25
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (30 bp):
AAATATATTTAAAAAATTAATGATACAATA
Found at i:40977353 original size:22 final size:22
Alignment explanation
Indices: 40977323--40977365 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
40977313 ACACCAAAAC
*
40977323 AGGCTTTTAGCGGCGCTTTTTT
1 AGGCCTTTAGCGGCGCTTTTTT
40977345 AGGCCTTTAGCGGCGCTTTTT
1 AGGCCTTTAGCGGCGCTTTTT
40977366 AGCGCTGCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.09, C:0.21, G:0.28, T:0.42
Consensus pattern (22 bp):
AGGCCTTTAGCGGCGCTTTTTT
Found at i:40977513 original size:43 final size:43
Alignment explanation
Indices: 40977459--40977728 Score: 391
Period size: 43 Copynumber: 6.3 Consensus size: 43
40977449 TTTTAGAAAT
40977459 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
* * * *
40977502 AAACGACGCTAAAGAACAAGACCTTTAGCGGCGCTTCTCCTAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
*
40977545 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTGTCCCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
* * *
40977588 AAACGCCGCTAAAAACCAAGACCTTTAGCGGTGCTTTTTCCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
* *
40977631 AAACGCCGCTAAAGACCAAGACCTTTAGCGACGCTTTTACCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
* * * *
40977674 AAACGCCGCTATAGATCAA-ACCTTTAGCGGCGCTTCTT-GCAA
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTT-TTCCCAC
40977716 AAACGCCGCTAAA
1 AAACGCCGCTAAA
40977729 AACATAACCT
Statistics
Matches: 204, Mismatches: 22, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
42 29 0.14
43 175 0.86
ACGTcount: A:0.31, C:0.32, G:0.18, T:0.19
Consensus pattern (43 bp):
AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
Found at i:40982855 original size:29 final size:29
Alignment explanation
Indices: 40982813--40982897 Score: 82
Period size: 29 Copynumber: 3.0 Consensus size: 29
40982803 NNNNNNNNNN
*
40982813 CTAACACTAAATCTATAAACCTTAAATCC
1 CTAACACTTAATCTATAAACCTTAAATCC
* * * *
40982842 CTAACTCTTAATCTCTAACCCTT-AACCC
1 CTAACACTTAATCTATAAACCTTAAATCC
* * * *
40982870 CTAACCCCTAACCCATAAACCTTAAATC
1 CTAACACTTAATCTATAAACCTTAAATC
40982898 ACAACCCTTA
Statistics
Matches: 43, Mismatches: 12, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
28 21 0.49
29 22 0.51
ACGTcount: A:0.38, C:0.35, G:0.00, T:0.27
Consensus pattern (29 bp):
CTAACACTTAATCTATAAACCTTAAATCC
Found at i:40982859 original size:14 final size:14
Alignment explanation
Indices: 40982832--40982908 Score: 59
Period size: 14 Copynumber: 5.4 Consensus size: 14
40982822 AATCTATAAA
40982832 CCTTAAATCCCTAAC
1 CCTT-AATCCCTAAC
* *
40982847 TCTTAATCTCTAAC
1 CCTTAATCCCTAAC
*
40982861 CCTTAACCCCTAAC
1 CCTTAATCCCTAAC
* *
40982875 CCCTAA-CCCATAAA
1 CCTTAATCCC-TAAC
*
40982889 CCTTAAATCAC-AAC
1 CCTT-AATCCCTAAC
40982903 CCTTAA
1 CCTTAA
40982909 ATCAGAATCC
Statistics
Matches: 49, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
13 5 0.10
14 37 0.76
15 5 0.10
16 2 0.04
ACGTcount: A:0.35, C:0.39, G:0.00, T:0.26
Consensus pattern (14 bp):
CCTTAATCCCTAAC
Found at i:40982931 original size:14 final size:15
Alignment explanation
Indices: 40982914--40982945 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
40982904 CTTAAATCAG
40982914 AATCCCTAA-TCCAT
1 AATCCCTAATTCCAT
40982928 AATCCCTAATTCCAT
1 AATCCCTAATTCCAT
40982943 AAT
1 AAT
40982946 TTATAAACCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.38, C:0.31, G:0.00, T:0.31
Consensus pattern (15 bp):
AATCCCTAATTCCAT
Found at i:40983047 original size:21 final size:21
Alignment explanation
Indices: 40982995--40983036 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 21
40982985 ATCCTAAATT
40982995 AACCATATATAT---ACCCTA
1 AACCATATATATAAAACCCTA
40983013 AACCATATATATAAAACCCTA
1 AACCATATATATAAAACCCTA
40983034 AAC
1 AAC
40983037 TATAATGATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 12 0.57
21 9 0.43
ACGTcount: A:0.50, C:0.26, G:0.00, T:0.24
Consensus pattern (21 bp):
AACCATATATATAAAACCCTA
Found at i:40983381 original size:41 final size:41
Alignment explanation
Indices: 40983324--40983703 Score: 591
Period size: 41 Copynumber: 9.2 Consensus size: 41
40983314 AATGTTCAAT
* *
40983324 TAAAGATCTGAGCATTAGCGACGCTTTCTCAAATACGCCGC
1 TAAAGATCTGAGCATTAGCGGCGCTTTCTCAAAAACGCCGC
* *
40983365 TAAAGATCTAAGCATTAGCGGCGCTTTCTCAAAAATGCCGC
1 TAAAGATCTGAGCATTAGCGGCGCTTTCTCAAAAACGCCGC
* * *
40983406 TAAAGATCTGACCATTAGCGGCGCTTTTTTAAAAACGCCGC
1 TAAAGATCTGAGCATTAGCGGCGCTTTCTCAAAAACGCCGC
*
40983447 TAAAGATCTGAGTATTAGCGGCGCTTTCTCAAAAACGCCGC
1 TAAAGATCTGAGCATTAGCGGCGCTTTCTCAAAAACGCCGC
* *
40983488 TAAAGATCTGAGCATTAGCGGCGCTTTTTTAAAAACGCCGC
1 TAAAGATCTGAGCATTAGCGGCGCTTTCTCAAAAACGCCGC
* * *
40983529 TAAAGATCTGAGCATAAGCGGCGCTTTTTTAAAAACGCCGC
1 TAAAGATCTGAGCATTAGCGGCGCTTTCTCAAAAACGCCGC
40983570 TAAAGATCTGAGCATTAGCGGCGCTTTCTCAAAAACGCCGC
1 TAAAGATCTGAGCATTAGCGGCGCTTTCTCAAAAACGCCGC
*
40983611 TAAAGATCTGAGCATTAACGGCGCTTTCTCAAAAACGCCGC
1 TAAAGATCTGAGCATTAGCGGCGCTTTCTCAAAAACGCCGC
* *
40983652 TAAAGATCTGAGCATTAGCGGCACTTTTTTTC-AAAACGCCGC
1 TAAAGATCTGAGCATTAGCGGCGC--TTTCTCAAAAACGCCGC
40983694 TAAAGATCTG
1 TAAAGATCTG
40983704 TAAGGTACAA
Statistics
Matches: 313, Mismatches: 24, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
41 288 0.92
42 20 0.06
43 5 0.02
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.25
Consensus pattern (41 bp):
TAAAGATCTGAGCATTAGCGGCGCTTTCTCAAAAACGCCGC
Found at i:40983785 original size:40 final size:40
Alignment explanation
Indices: 40983736--40983870 Score: 148
Period size: 40 Copynumber: 3.4 Consensus size: 40
40983726 GGGCTTAGAC
*
40983736 TTTTT-GCGGCGTTTTTCCAAAAAACGCCGCTAATGCT-AA
1 TTTTTAGCGGCG-TTTTCCAAAAAACGCCGCTAATGCTCGA
* * *
40983775 TTTTTAGCGGCGCTTTCCTAGAAACGCCGCTAATGCTCGA
1 TTTTTAGCGGCGTTTTCCAAAAAACGCCGCTAATGCTCGA
* * ** * *
40983815 TCTTTAGCGGCGTTTTACGTAAAGCACCGCTAATGCTCGA
1 TTTTTAGCGGCGTTTTCCAAAAAACGCCGCTAATGCTCGA
*
40983855 TTTTTAGTGGCGTTTT
1 TTTTTAGCGGCGTTTT
40983871 TTGTCCAAAC
Statistics
Matches: 80, Mismatches: 14, Indels: 3
0.82 0.14 0.03
Matches are distributed among these distances:
39 27 0.34
40 53 0.66
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.35
Consensus pattern (40 bp):
TTTTTAGCGGCGTTTTCCAAAAAACGCCGCTAATGCTCGA
Found at i:40984115 original size:44 final size:44
Alignment explanation
Indices: 40984064--40984147 Score: 159
Period size: 44 Copynumber: 1.9 Consensus size: 44
40984054 TTGAAATAAA
*
40984064 ATAGAAGTTGTGATAATTATACATTTAAAAATAATTATAACTTG
1 ATAGAAGTTGTGATAATTACACATTTAAAAATAATTATAACTTG
40984108 ATAGAAGTTGTGATAATTACACATTTAAAAATAATTATAA
1 ATAGAAGTTGTGATAATTACACATTTAAAAATAATTATAA
40984148 TTTAAATTAC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.48, C:0.05, G:0.11, T:0.37
Consensus pattern (44 bp):
ATAGAAGTTGTGATAATTACACATTTAAAAATAATTATAACTTG
Found at i:40984143 original size:18 final size:17
Alignment explanation
Indices: 40984120--40984153 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
40984110 AGAAGTTGTG
40984120 ATAATTACACATTTAAAA
1 ATAATTACA-ATTTAAAA
*
40984138 ATAATTATAATTTAAA
1 ATAATTACAATTTAAA
40984154 TTACAATTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (17 bp):
ATAATTACAATTTAAAA
Found at i:40986001 original size:49 final size:49
Alignment explanation
Indices: 40985929--40986024 Score: 192
Period size: 49 Copynumber: 2.0 Consensus size: 49
40985919 AACCTATCAC
40985929 ACCAAATAGGACTACTAGAGACCATCCATTCAATCACACCAATATGTGG
1 ACCAAATAGGACTACTAGAGACCATCCATTCAATCACACCAATATGTGG
40985978 ACCAAATAGGACTACTAGAGACCATCCATTCAATCACACCAATATGT
1 ACCAAATAGGACTACTAGAGACCATCCATTCAATCACACCAATATGT
40986025 TGTGGTATAC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.40, C:0.27, G:0.12, T:0.21
Consensus pattern (49 bp):
ACCAAATAGGACTACTAGAGACCATCCATTCAATCACACCAATATGTGG
Found at i:40987082 original size:14 final size:14
Alignment explanation
Indices: 40987063--40987127 Score: 60
Period size: 14 Copynumber: 4.4 Consensus size: 14
40987053 TTGGCAAAGC
40987063 AAGAAAGAAGAGAA
1 AAGAAAGAAGAGAA
40987077 AAGAAAGAAGAAGAA
1 AAGAAAGAAG-AGAA
* *
40987092 AAGGAAAATAACAGAA
1 AA-G-AAAGAAGAGAA
*
40987108 ACATAAAGAA-AGAA
1 A-AGAAAGAAGAGAA
40987122 AAGAAA
1 AAGAAA
40987128 AATGTGCAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
13 4 0.10
14 15 0.36
15 11 0.26
16 6 0.14
17 6 0.14
ACGTcount: A:0.72, C:0.03, G:0.22, T:0.03
Consensus pattern (14 bp):
AAGAAAGAAGAGAA
Found at i:40992867 original size:5 final size:5
Alignment explanation
Indices: 40992857--40992889 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
40992847 TAATATAATC
*
40992857 TTAAA TGAAA -TAAA TTAAA TTAAA TTAAA TTAA
1 TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA TTAA
40992890 TTCTATAGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
4 3 0.12
5 22 0.88
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (5 bp):
TTAAA
Found at i:40995033 original size:20 final size:20
Alignment explanation
Indices: 40995010--40995047 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
40995000 GATGAAAACG
40995010 ACATTTGAATTATGATTTAA
1 ACATTTGAATTATGATTTAA
* *
40995030 ACATTTGATTTATTATTT
1 ACATTTGAATTATGATTT
40995048 TTAGGAAAAA
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:0.34, C:0.05, G:0.08, T:0.53
Consensus pattern (20 bp):
ACATTTGAATTATGATTTAA
Found at i:41004778 original size:15 final size:15
Alignment explanation
Indices: 41004758--41004800 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
41004748 ATGATTTTAA
*
41004758 TGGAATGTAATTTTT
1 TGGAATGTAATTGTT
*
41004773 TGGAATGTAGTTGTT
1 TGGAATGTAATTGTT
* *
41004788 GGGAATGTGATTG
1 TGGAATGTAATTG
41004801 CTTGAAAAGT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.23, C:0.00, G:0.33, T:0.44
Consensus pattern (15 bp):
TGGAATGTAATTGTT
Found at i:41005820 original size:17 final size:17
Alignment explanation
Indices: 41005800--41005837 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
41005790 TATAAAATAT
*
41005800 AATTTATAA-TAATTATA
1 AATTTAAAACTAATTA-A
41005817 AATTTAAAACTAATTAA
1 AATTTAAAACTAATTAA
41005834 AATT
1 AATT
41005838 AATTAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (17 bp):
AATTTAAAACTAATTAA
Found at i:41010119 original size:15 final size:15
Alignment explanation
Indices: 41010101--41010134 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
41010091 CAAACAGATG
41010101 GAAAACAAAAAAAAA
1 GAAAACAAAAAAAAA
* *
41010116 GAAAAGAAAAACAAA
1 GAAAACAAAAAAAAA
41010131 GAAA
1 GAAA
41010135 CAAGGCCACT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.82, C:0.06, G:0.12, T:0.00
Consensus pattern (15 bp):
GAAAACAAAAAAAAA
Found at i:41011133 original size:16 final size:15
Alignment explanation
Indices: 41011105--41011174 Score: 68
Period size: 16 Copynumber: 4.4 Consensus size: 15
41011095 GTTTGATTAC
*
41011105 TATAATAGAATAGTGT
1 TATAATAG-ATAGAGT
*
41011121 TGTAATTAGATAGAGT
1 TATAA-TAGATAGAGT
*
41011137 TATAATAGATTAAAGT
1 TATAATAGA-TAGAGT
*
41011153 TATAATAGAATAGAGC
1 TATAATAG-ATAGAGT
41011169 TATAAT
1 TATAAT
41011175 CAGTAATTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
15 4 0.09
16 37 0.82
17 4 0.09
ACGTcount: A:0.46, C:0.01, G:0.17, T:0.36
Consensus pattern (15 bp):
TATAATAGATAGAGT
Found at i:41011432 original size:23 final size:21
Alignment explanation
Indices: 41011401--41011443 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
41011391 CATTATATGA
41011401 ATTAAAAAATCATAATATATAAT
1 ATTAAAAAA--ATAATATATAAT
*
41011424 ATTATAAAAATAATATATAA
1 ATTAAAAAAATAATATATAA
41011444 CCTACTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 11 0.58
23 8 0.42
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (21 bp):
ATTAAAAAAATAATATATAAT
Found at i:41020759 original size:16 final size:17
Alignment explanation
Indices: 41020732--41020767 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
41020722 AAAGAGTTGA
41020732 GAGAGAGGATGAGAGAT
1 GAGAGAGGATGAGAGAT
*
41020749 GAGAG-GGATGAGGGAT
1 GAGAGAGGATGAGAGAT
41020765 GAG
1 GAG
41020768 GGATGATTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.36, C:0.00, G:0.53, T:0.11
Consensus pattern (17 bp):
GAGAGAGGATGAGAGAT
Found at i:41024841 original size:20 final size:20
Alignment explanation
Indices: 41024816--41024853 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
41024806 ACCCCCTTTA
41024816 TTAACATAAA-AATTTAAAAT
1 TTAACA-AAATAATTTAAAAT
41024836 TTAACAAAATAATTTAAA
1 TTAACAAAATAATTTAAA
41024854 CTAGAAAAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (20 bp):
TTAACAAAATAATTTAAAAT
Found at i:41031651 original size:16 final size:17
Alignment explanation
Indices: 41031624--41031658 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
41031614 AGAGAGTTGA
41031624 GAGAGAGGATGAGAGAT
1 GAGAGAGGATGAGAGAT
*
41031641 GAGAG-GGATGAGGGAT
1 GAGAGAGGATGAGAGAT
41031657 GA
1 GA
41031659 TTGAAAAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.37, C:0.00, G:0.51, T:0.11
Consensus pattern (17 bp):
GAGAGAGGATGAGAGAT
Found at i:41041614 original size:17 final size:18
Alignment explanation
Indices: 41041592--41041625 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
41041582 CAAATATTTA
41041592 AAAATT-ATAAAAAATTC
1 AAAATTAATAAAAAATTC
41041609 AAAATTAATAAAAAATT
1 AAAATTAATAAAAAATT
41041626 ATAAAAAGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (18 bp):
AAAATTAATAAAAAATTC
Found at i:41041650 original size:28 final size:25
Alignment explanation
Indices: 41041582--41041651 Score: 68
Period size: 28 Copynumber: 2.5 Consensus size: 25
41041572 ACCACATCAA
41041582 CAAATATTTAAAAATTATAAAAAATT
1 CAAA-ATTTAAAAATTATAAAAAATT
*
41041608 CAAAATTAATAAAAAATTATAAAAAGTT
1 CAAAATT--T-AAAAATTATAAAAAATT
41041636 CATAAAATTTCAAAAA
1 C--AAAATTT-AAAAA
41041652 AAAAAAGTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
25 3 0.08
26 4 0.11
27 1 0.03
28 23 0.62
30 6 0.16
ACGTcount: A:0.63, C:0.06, G:0.01, T:0.30
Consensus pattern (25 bp):
CAAAATTTAAAAATTATAAAAAATT
Found at i:41043141 original size:41 final size:41
Alignment explanation
Indices: 41043080--41043193 Score: 174
Period size: 41 Copynumber: 2.8 Consensus size: 41
41043070 TTAATTTAAA
* * *
41043080 CAGATTCAACGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
1 CAGA-TCACCGGCACGTAGCCTGCTAGGCTTATAACCTGATT
*
41043122 CAGATCACCGGCACGTAGCCTGCTAGGTTTATAACCTGATT
1 CAGATCACCGGCACGTAGCCTGCTAGGCTTATAACCTGATT
*
41043163 CAGATCACCGGCACGTAGCCTGCTAGACTTA
1 CAGATCACCGGCACGTAGCCTGCTAGGCTTA
41043194 AAGTCTGAAA
Statistics
Matches: 66, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
41 62 0.94
42 4 0.06
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (41 bp):
CAGATCACCGGCACGTAGCCTGCTAGGCTTATAACCTGATT
Found at i:41048592 original size:41 final size:41
Alignment explanation
Indices: 41048535--41048702 Score: 164
Period size: 41 Copynumber: 4.1 Consensus size: 41
41048525 TTAAAGTGAT
* *
41048535 TGAAATAATTTAGACTTTACGTCTAGCAGGCTTGATGCCGG
1 TGAAATAATTCAGACTTTACGTCTAGCAGGCTTAATGCCGG
41048576 TGAAATAATTCAGACTTTACGTCTAGCAGGCTTAATGCCGG
1 TGAAATAATTCAGACTTTACGTCTAGCAGGCTTAATGCCGG
* * *
41048617 TG--ATACATATCGGACTATATGTCTAGCAGGC-TAAGTGCCGG
1 TGAAATA-AT-TCAGACTTTACGTCTAGCAGGCTTAA-TGCCGG
* * * * * * *
41048658 TGTATTGAA-TCAGGCTTTAAGCCTAGCAGGCTAAATACCGG
1 TGAAAT-AATTCAGACTTTACGTCTAGCAGGCTTAATGCCGG
41048699 TGAA
1 TGAA
41048703 TCTGTTTTTA
Statistics
Matches: 106, Mismatches: 14, Indels: 14
0.79 0.10 0.10
Matches are distributed among these distances:
39 3 0.03
40 5 0.05
41 93 0.88
42 2 0.02
43 2 0.02
44 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (41 bp):
TGAAATAATTCAGACTTTACGTCTAGCAGGCTTAATGCCGG
Found at i:41051470 original size:22 final size:22
Alignment explanation
Indices: 41051407--41051472 Score: 105
Period size: 22 Copynumber: 3.0 Consensus size: 22
41051397 GTGACCGAAA
**
41051407 AACGTACTAAGCTCTCATGGCT
1 AACGTACTAAGCTCTCATGTTT
41051429 AACGTACTAAGCTCTCATGTTT
1 AACGTACTAAGCTCTCATGTTT
*
41051451 CACGTACTAAGCTCTCATGTTT
1 AACGTACTAAGCTCTCATGTTT
41051473 GAACAATAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.33
Consensus pattern (22 bp):
AACGTACTAAGCTCTCATGTTT
Found at i:41058039 original size:14 final size:14
Alignment explanation
Indices: 41058020--41058049 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
41058010 ACAGCTAGAT
41058020 TTATATATACTTGG
1 TTATATATACTTGG
41058034 TTATATATACTTGG
1 TTATATATACTTGG
41058048 TT
1 TT
41058050 CATCCCTTCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.27, C:0.07, G:0.13, T:0.53
Consensus pattern (14 bp):
TTATATATACTTGG
Found at i:41060741 original size:20 final size:20
Alignment explanation
Indices: 41060716--41060760 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
41060706 TAAGTTCACA
41060716 TAATTAAAAC-AAGACAC-AAT
1 TAATT-AAACTAAGAC-CTAAT
41060736 TAATTAAACTAAGACCTAAT
1 TAATTAAACTAAGACCTAAT
41060756 TAATT
1 TAATT
41060761 CGGTTTGGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 5 0.22
20 18 0.78
ACGTcount: A:0.53, C:0.13, G:0.04, T:0.29
Consensus pattern (20 bp):
TAATTAAACTAAGACCTAAT
Found at i:41063092 original size:20 final size:20
Alignment explanation
Indices: 41063059--41063102 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
41063049 TAAGTTCACA
41063059 TAATTAAAACAAGACAC-AAT
1 TAATTAAAACAAGAC-CTAAT
41063079 TAATT-AAACTAAGACCTAAT
1 TAATTAAAAC-AAGACCTAAT
41063099 TAAT
1 TAAT
41063103 CCAGTTTGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.55, C:0.14, G:0.05, T:0.27
Consensus pattern (20 bp):
TAATTAAAACAAGACCTAAT
Found at i:41064656 original size:17 final size:17
Alignment explanation
Indices: 41064624--41064663 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
41064614 GTTTTCATTG
*
41064624 AAACTTCTTGAAATTTC
1 AAACTTCTTGAAATTTA
**
41064641 AAACTTCTTGCCATTTA
1 AAACTTCTTGAAATTTA
41064658 AAACTT
1 AAACTT
41064664 GTACAAAACC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.35, C:0.20, G:0.05, T:0.40
Consensus pattern (17 bp):
AAACTTCTTGAAATTTA
Found at i:41065475 original size:22 final size:22
Alignment explanation
Indices: 41065421--41065475 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
41065411 ATCTAGTAAC
41065421 CAGAATGGCTAAGAGCCATAAA
1 CAGAATGGCTAAGAGCCATAAA
* * *
41065443 CAGGATAGCTATA-AGCTATAAA
1 CAGAATGGCTA-AGAGCCATAAA
*
41065465 TAGAATGGCTA
1 CAGAATGGCTA
41065476 CAATCCATAA
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
22 25 0.96
23 1 0.04
ACGTcount: A:0.44, C:0.15, G:0.22, T:0.20
Consensus pattern (22 bp):
CAGAATGGCTAAGAGCCATAAA
Found at i:41065538 original size:32 final size:32
Alignment explanation
Indices: 41065480--41065646 Score: 169
Period size: 32 Copynumber: 5.3 Consensus size: 32
41065470 TGGCTACAAT
* *
41065480 CCATAAGT-ACAGTAATAT-ATTGGCACAAAG
1 CCATCAGTAACAGTAATATGATCGGCACAAAG
* * * * *
41065510 CCATCAGTAGCAGTGATATGACCAGCACACAG
1 CCATCAGTAACAGTAATATGATCGGCACAAAG
* *
41065542 CCATCAATAAC-GATAATATGATCGGTACAAAG
1 CCATCAGTAACAG-TAATATGATCGGCACAAAG
**
41065574 CCATCAGTAATGGTAATATGATCGGCACAAAG
1 CCATCAGTAACAGTAATATGATCGGCACAAAG
* * * *
41065606 CCATTAGTAACGGTAATATGATCGGTAAAAAG
1 CCATCAGTAACAGTAATATGATCGGCACAAAG
41065638 CCATCAGTA
1 CCATCAGTA
41065647 GCATCATAGC
Statistics
Matches: 111, Mismatches: 22, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
30 7 0.06
31 9 0.08
32 94 0.85
33 1 0.01
ACGTcount: A:0.40, C:0.20, G:0.19, T:0.22
Consensus pattern (32 bp):
CCATCAGTAACAGTAATATGATCGGCACAAAG
Found at i:41065608 original size:64 final size:64
Alignment explanation
Indices: 41065504--41065646 Score: 187
Period size: 64 Copynumber: 2.2 Consensus size: 64
41065494 ATATATTGGC
* * *
41065504 ACAAAGCCATCAGTAGCAGTGATATGACCAGCACACAGCCATCAATAACGATAATATGATCGGT
1 ACAAAGCCATCAGTAACAGTAATATGACCAGCACAAAGCCATCAATAACGATAATATGATCGGT
** * * * * *
41065568 ACAAAGCCATCAGTAATGGTAATATGATCGGCACAAAGCCATTAGTAACGGTAATATGATCGGT
1 ACAAAGCCATCAGTAACAGTAATATGACCAGCACAAAGCCATCAATAACGATAATATGATCGGT
*
41065632 AAAAAGCCATCAGTA
1 ACAAAGCCATCAGTA
41065647 GCATCATAGC
Statistics
Matches: 68, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
64 68 1.00
ACGTcount: A:0.40, C:0.20, G:0.20, T:0.20
Consensus pattern (64 bp):
ACAAAGCCATCAGTAACAGTAATATGACCAGCACAAAGCCATCAATAACGATAATATGATCGGT
Found at i:41065853 original size:24 final size:24
Alignment explanation
Indices: 41065818--41065896 Score: 140
Period size: 24 Copynumber: 3.3 Consensus size: 24
41065808 CCATGCTTAG
* *
41065818 AATCAGTCATACAAATCACAGACC
1 AATCAGTGATACAAATCACAGACA
41065842 AATCAGTGATACAAATCACAGACA
1 AATCAGTGATACAAATCACAGACA
41065866 AATCAGTGATACAAATCACAGACA
1 AATCAGTGATACAAATCACAGACA
41065890 AATCAGT
1 AATCAGT
41065897 CATTTACATC
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 53 1.00
ACGTcount: A:0.48, C:0.23, G:0.11, T:0.18
Consensus pattern (24 bp):
AATCAGTGATACAAATCACAGACA
Found at i:41065868 original size:11 final size:11
Alignment explanation
Indices: 41065828--41065894 Score: 53
Period size: 11 Copynumber: 5.7 Consensus size: 11
41065818 AATCAGTCAT
41065828 ACAAATCACAG
1 ACAAATCACAG
* * *
41065839 ACCAATCAGTGAT
1 ACAAATCA--CAG
41065852 ACAAATCACAG
1 ACAAATCACAG
* *
41065863 ACAAATCAGTGAT
1 ACAAATCA--CAG
41065876 ACAAATCACAG
1 ACAAATCACAG
41065887 ACAAATCA
1 ACAAATCA
41065895 GTCATTTACA
Statistics
Matches: 42, Mismatches: 10, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
11 25 0.60
13 17 0.40
ACGTcount: A:0.51, C:0.24, G:0.10, T:0.15
Consensus pattern (11 bp):
ACAAATCACAG
Found at i:41065881 original size:13 final size:13
Alignment explanation
Indices: 41065842--41065883 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
41065832 ATCACAGACC
41065842 AATCAGTGATACA
1 AATCAGTGATACA
* *
41065855 AATCA--CAGACA
1 AATCAGTGATACA
41065866 AATCAGTGATACA
1 AATCAGTGATACA
41065879 AATCA
1 AATCA
41065884 CAGACAAATC
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
11 9 0.39
13 14 0.61
ACGTcount: A:0.50, C:0.19, G:0.12, T:0.19
Consensus pattern (13 bp):
AATCAGTGATACA
Found at i:41065913 original size:24 final size:24
Alignment explanation
Indices: 41065818--41065928 Score: 105
Period size: 24 Copynumber: 4.6 Consensus size: 24
41065808 CCATGCTTAG
** *
41065818 AATCAGTCATACAAATCACAGACC
1 AATCAGTCATTTAAATCACAGACA
* **
41065842 AATCAGTGATACAAATCACAGACA
1 AATCAGTCATTTAAATCACAGACA
* **
41065866 AATCAGTGATACAAATCACAGACA
1 AATCAGTCATTTAAATCACAGACA
* *
41065890 AATCAGTCATTTACATCACGGACA
1 AATCAGTCATTTAAATCACAGACA
* *
41065914 TATCAATCATTTAAA
1 AATCAGTCATTTAAA
41065929 CTCGAGGGGC
Statistics
Matches: 77, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 77 1.00
ACGTcount: A:0.46, C:0.23, G:0.10, T:0.22
Consensus pattern (24 bp):
AATCAGTCATTTAAATCACAGACA
Found at i:41066043 original size:81 final size:79
Alignment explanation
Indices: 41065945--41066223 Score: 281
Period size: 81 Copynumber: 3.5 Consensus size: 79
41065935 GGGCAAAATT
* * * * *
41065945 GTCA-TTTACCCTCTAGGGGCATTACGATTATTTGACCTTACAGGGGTATTTCAGTCATTTAACC
1 GTCATTTTACCCTATAGGGGCATTACGATCATTTTACCCTACGGGGGTATTTC-GTCATTTAACC
*
41066009 CTATCAGGGTACTACG
65 CTAT-AGGGTATTACG
* * * *
41066025 GTCATTTTACCCTATAGGGGCATTATGGTCATTTTACCCTATGGGGGTTTTTCGATCATTTAACC
1 GTCATTTTACCCTATAGGGGCATTACGATCATTTTACCCTACGGGGGTATTTCG-TCATTTAACC
41066090 CTATAGGGGTATTACG
65 CTATA-GGGTATTACG
* * * * * * *
41066106 GTCATTTTACCTTACAGAGGCATTACGATCATTTTACCCTACGGGGGCATTACGGTCATTTTAGC
1 GTCATTTTACCCTATAGGGGCATTACGATCATTTTACCCTACGGGGGTATTTC-GTCATTTAACC
* * *
41066171 CTATGGGAGTTTTTCG
65 CTATAGG-GTATTACG
* * * *
41066187 ATCATTTTACCCTATATGGGTATTACGATCAGTTTAC
1 GTCATTTTACCCTATAGGGGCATTACGATCATTTTAC
41066224 AAATAATGGG
Statistics
Matches: 163, Mismatches: 31, Indels: 9
0.80 0.15 0.04
Matches are distributed among these distances:
80 8 0.05
81 154 0.94
82 1 0.01
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.37
Consensus pattern (79 bp):
GTCATTTTACCCTATAGGGGCATTACGATCATTTTACCCTACGGGGGTATTTCGTCATTTAACCC
TATAGGGTATTACG
Found at i:41066211 original size:108 final size:108
Alignment explanation
Indices: 41066021--41066223 Score: 316
Period size: 108 Copynumber: 1.9 Consensus size: 108
41066011 ATCAGGGTAC
* * * *
41066021 TACGGTCATTTTACCCTATAGGGGCATTATGGTCATTTTACCCTATGGGGGTTTTTCGATCATTT
1 TACGATCATTTTACCCTACAGGGGCATTACGGTCATTTTACCCTATGGGAGTTTTTCGATCATTT
* *
41066086 AACCCTATAGGGGTATTACGGTCATTTTACCTTACAGAGGCAT
66 AACCCTATAGGGGTATTACGATCAGTTTACCTTACAGAGGCAT
* *
41066129 TACGATCATTTTACCCTACGGGGGCATTACGGTCATTTTAGCCTATGGGAGTTTTTCGATCATTT
1 TACGATCATTTTACCCTACAGGGGCATTACGGTCATTTTACCCTATGGGAGTTTTTCGATCATTT
* *
41066194 TACCCTATATGGGTATTACGATCAGTTTAC
66 AACCCTATAGGGGTATTACGATCAGTTTAC
41066224 AAATAATGGG
Statistics
Matches: 85, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
108 85 1.00
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.37
Consensus pattern (108 bp):
TACGATCATTTTACCCTACAGGGGCATTACGGTCATTTTACCCTATGGGAGTTTTTCGATCATTT
AACCCTATAGGGGTATTACGATCAGTTTACCTTACAGAGGCAT
Found at i:41066215 original size:27 final size:27
Alignment explanation
Indices: 41065949--41066223 Score: 223
Period size: 27 Copynumber: 10.2 Consensus size: 27
41065939 AAAATTGTCA
* * *
41065949 TTTACCCTCTAGGGGCATTACGATTAT
1 TTTACCCTATAGGGGTATTACGATCAT
* * * *
41065976 TTGACCTTACAGGGGTATTTC-AGTCAT
1 TTTACCCTATAGGGGTATTACGA-TCAT
* * *
41066003 TTAACCCTATCA-GGGTACTACGGTCAT
1 TTTACCCTAT-AGGGGTATTACGATCAT
* * *
41066030 TTTACCCTATAGGGGCATTATGGTCAT
1 TTTACCCTATAGGGGTATTACGATCAT
* * *
41066057 TTTACCCTATGGGGGTTTTTCGATCAT
1 TTTACCCTATAGGGGTATTACGATCAT
* *
41066084 TTAACCCTATAGGGGTATTACGGTCAT
1 TTTACCCTATAGGGGTATTACGATCAT
* * * *
41066111 TTTACCTTACAGAGGCATTACGATCAT
1 TTTACCCTATAGGGGTATTACGATCAT
** * *
41066138 TTTACCCTACGGGGGCATTACGGTCAT
1 TTTACCCTATAGGGGTATTACGATCAT
* * *
41066165 TTTAGCCTAT-GGGAGTTTTTCGATCAT
1 TTTACCCTATAGGG-GTATTACGATCAT
* *
41066192 TTTACCCTATATGGGTATTACGATCAG
1 TTTACCCTATAGGGGTATTACGATCAT
41066219 TTTAC
1 TTTAC
41066224 AAATAATGGG
Statistics
Matches: 193, Mismatches: 49, Indels: 12
0.76 0.19 0.05
Matches are distributed among these distances:
26 5 0.03
27 185 0.96
28 3 0.02
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.37
Consensus pattern (27 bp):
TTTACCCTATAGGGGTATTACGATCAT
Found at i:41068749 original size:46 final size:46
Alignment explanation
Indices: 41068664--41068751 Score: 115
Period size: 46 Copynumber: 1.9 Consensus size: 46
41068654 AAAAGTGCAG
* * *
41068664 TGTGGGCCTTAGCCCATTACAGTATCAGAATTAGAAATAGAATACA
1 TGTGGGCCTAAGCCCAATACAGTATCAGAATCAGAAATAGAATACA
* *
41068710 TGTGGGCCTAAGCCCAATACAGT-TACATAATCAGTAATAGAA
1 TGTGGGCCTAAGCCCAATACAGTAT-CAGAATCAGAAATAGAA
41068752 ATGCAACAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
45 1 0.03
46 35 0.97
ACGTcount: A:0.38, C:0.18, G:0.19, T:0.25
Consensus pattern (46 bp):
TGTGGGCCTAAGCCCAATACAGTATCAGAATCAGAAATAGAATACA
Found at i:41069005 original size:32 final size:32
Alignment explanation
Indices: 41068950--41069111 Score: 159
Period size: 32 Copynumber: 5.1 Consensus size: 32
41068940 GGATACAAGT
* * *
41068950 CATAAGT-ATAGTAATCTGATTGGCACAAAGC
1 CATAAGTAACAGTAATATGATCGGCACAAAGC
* * * *
41068981 CATAAGTAGCAGTGATATGATTGGCACACAGC
1 CATAAGTAACAGTAATATGATCGGCACAAAGC
* * *
41069013 CAT-CGCTAACGGTAATATGATCGGCACAAATC
1 CATAAG-TAACAGTAATATGATCGGCACAAAGC
* *
41069045 CATAAGTAACGGCAATATGATCGGCACAAAGC
1 CATAAGTAACAGTAATATGATCGGCACAAAGC
* *
41069077 CATCAA-TAACAGAAATATGACCGGCACAAAGC
1 CAT-AAGTAACAGTAATATGATCGGCACAAAGC
41069109 CAT
1 CAT
41069112 CAATAGCATC
Statistics
Matches: 109, Mismatches: 18, Indels: 7
0.81 0.13 0.05
Matches are distributed among these distances:
31 8 0.07
32 98 0.90
33 3 0.03
ACGTcount: A:0.39, C:0.22, G:0.20, T:0.20
Consensus pattern (32 bp):
CATAAGTAACAGTAATATGATCGGCACAAAGC
Found at i:41069063 original size:64 final size:64
Alignment explanation
Indices: 41068959--41069111 Score: 180
Period size: 64 Copynumber: 2.4 Consensus size: 64
41068949 TCATAAGTAT
* * * ** * * **
41068959 AGTAATCTGATTGGCACAAAGCCATAAGTAGCAGTGATATGATTGGCACACAGCCATCGCTAAC
1 AGTAATATGATCGGCACAAAGCCATAAGTAACAGCAATATGATCGGCACAAAGCCATCAATAAC
* * *
41069023 GGTAATATGATCGGCACAAATCCATAAGTAACGGCAATATGATCGGCACAAAGCCATCAATAAC
1 AGTAATATGATCGGCACAAAGCCATAAGTAACAGCAATATGATCGGCACAAAGCCATCAATAAC
* *
41069087 AGAAATATGACCGGCACAAAGCCAT
1 AGTAATATGATCGGCACAAAGCCAT
41069112 CAATAGCATC
Statistics
Matches: 73, Mismatches: 16, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
64 73 1.00
ACGTcount: A:0.39, C:0.22, G:0.20, T:0.19
Consensus pattern (64 bp):
AGTAATATGATCGGCACAAAGCCATAAGTAACAGCAATATGATCGGCACAAAGCCATCAATAAC
Found at i:41069329 original size:24 final size:24
Alignment explanation
Indices: 41069245--41069326 Score: 110
Period size: 24 Copynumber: 3.4 Consensus size: 24
41069235 CCATGCTCAG
41069245 AATCAGTCATACAAATCATAGACA
1 AATCAGTCATACAAATCATAGACA
* *
41069269 AATCAGTCATACCAATCACAGACA
1 AATCAGTCATACAAATCATAGACA
* ** *
41069293 AATCAGTCCTTTAAATCATAGAAA
1 AATCAGTCATACAAATCATAGACA
41069317 AATCAGTCAT
1 AATCAGTCAT
41069327 TTACATCACG
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 49 1.00
ACGTcount: A:0.46, C:0.22, G:0.09, T:0.23
Consensus pattern (24 bp):
AATCAGTCATACAAATCATAGACA
Found at i:41069389 original size:26 final size:25
Alignment explanation
Indices: 41069347--41069409 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 25
41069337 AACATATCAA
*
41069347 TCATTTACACTCGAGGGGCATTATAG
1 TCATTTAC-CTCGAGGGGCATTACAG
* *
41069373 TCATTTAACCTCTAGGGGCATTACGG
1 TCATTT-ACCTCGAGGGGCATTACAG
41069399 TCATTTTACCT
1 TCA-TTTACCT
41069410 TACAAAAGTA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
26 27 0.84
27 5 0.16
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.35
Consensus pattern (25 bp):
TCATTTACCTCGAGGGGCATTACAG
Found at i:41069447 original size:27 final size:26
Alignment explanation
Indices: 41069360--41069596 Score: 111
Period size: 27 Copynumber: 8.8 Consensus size: 26
41069350 TTTACACTCG
* * * *
41069360 AGGGGCATTATAGTCATTTAACCTCT
1 AGGGGTATTACAGTCATTTTACCTAT
* * *
41069386 AGGGGCATTACGGTCATTTTACCTTAC
1 AGGGGTATTACAGTCATTTTACC-TAT
*** * *
41069413 AAAAGTATTTCAGTCATTTAACTCTAT
1 AGGGGTATTACAGTCATTTTAC-CTAT
41069440 AGGGGTATTAC-GATCATTTTACCCTAT
1 AGGGGTATTACAG-TCATTTTA-CCTAT
* * * * *
41069467 AGAGGTCTTTCAATCATTTTACCTTAG
1 AGGGGTATTACAGTCATTTTACC-TAT
*
41069494 AGGGGTATTACGGTCATTTTACCT-T
1 AGGGGTATTACAGTCATTTTACCTAT
* * *
41069519 ACTGGGGCT-TTACGGTTATTTTATCCTAC
1 A--GGGG-TATTACAGTCATTTTA-CCTAT
* * *
41069548 GGGGGCATTACGGTCATTTTACCCTAT
1 AGGGGTATTACAGTCATTTTA-CCTAT
* * * *
41069575 TGGGTTATTATAATCATTTTAC
1 AGGGGTATTACAGTCATTTTAC
41069597 AAATCTTGGG
Statistics
Matches: 157, Mismatches: 42, Indels: 24
0.70 0.19 0.11
Matches are distributed among these distances:
25 1 0.01
26 25 0.16
27 125 0.80
28 6 0.04
ACGTcount: A:0.24, C:0.18, G:0.19, T:0.39
Consensus pattern (26 bp):
AGGGGTATTACAGTCATTTTACCTAT
Found at i:41069457 original size:54 final size:53
Alignment explanation
Indices: 41069371--41069520 Score: 183
Period size: 54 Copynumber: 2.8 Consensus size: 53
41069361 GGGGCATTAT
* *
41069371 AGTCATTTAACCTCTAGGGGCATTACGGTCATTTTACCTTACAAAAGTATTTC
1 AGTCATTTAACCTATAGGGGTATTACGGTCATTTTACCTTACAAAAGTATTTC
* * * * * *
41069424 AGTCATTTAACTCTATAGGGGTATTACGATCATTTTACCCTATAGAGGTCTTTC
1 AGTCATTTAAC-CTATAGGGGTATTACGGTCATTTTACCTTACAAAAGTATTTC
* * *
41069478 AATCATTTTACCTTAGAGGGGTATTACGGTCATTTTACCTTAC
1 AGTCATTTAACC-TATAGGGGTATTACGGTCATTTTACCTTAC
41069521 TGGGGCTTTA
Statistics
Matches: 81, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
53 12 0.15
54 69 0.85
ACGTcount: A:0.27, C:0.19, G:0.16, T:0.38
Consensus pattern (53 bp):
AGTCATTTAACCTATAGGGGTATTACGGTCATTTTACCTTACAAAAGTATTTC
Found at i:41069594 original size:54 final size:53
Alignment explanation
Indices: 41069440--41069596 Score: 149
Period size: 54 Copynumber: 2.9 Consensus size: 53
41069430 TTAACTCTAT
*
41069440 AGGGGTATTACGATCATTTTACCCTATAGAGGTCTTT-CAATCATTTTACCTTAG
1 AGGGGTATTACGGTCATTTTACCCTATAG-GGT-TTTACAATCATTTTACCTTAG
* * * ** *
41069494 AGGGGTATTACGGTCATTTTACCTTACTGGGGCTTTACGGTTATTTTATCC-TACG
1 AGGGGTATTACGGTCATTTTACCCTA-TAGGGTTTTACAATCATTTTA-CCTTA-G
* * *
41069549 -GGGGCATTACGGTCATTTTACCCTATTGGGTTATTATAATCATTTTAC
1 AGGGGTATTACGGTCATTTTACCCTATAGGGTT-TTACAATCATTTTAC
41069597 AAATCTTGGG
Statistics
Matches: 83, Mismatches: 15, Indels: 11
0.76 0.14 0.10
Matches are distributed among these distances:
53 9 0.11
54 69 0.83
55 5 0.06
ACGTcount: A:0.22, C:0.18, G:0.20, T:0.40
Consensus pattern (53 bp):
AGGGGTATTACGGTCATTTTACCCTATAGGGTTTTACAATCATTTTACCTTAG
Found at i:41072357 original size:41 final size:40
Alignment explanation
Indices: 41072312--41072392 Score: 92
Period size: 40 Copynumber: 2.0 Consensus size: 40
41072302 TGTTACTGAA
* *
41072312 TACTGCATGA-CTGCTACTGATACTATGATGGACTAAGGCCC
1 TACTGCAT-ATCTGATACTG-TACTAAGATGGACTAAGGCCC
* * *
41072353 TACTGTATATTTGATACTGTACTAAGATGGTCTAAGGCCC
1 TACTGCATATCTGATACTGTACTAAGATGGACTAAGGCCC
41072393 AAACTATTAC
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
40 20 0.59
41 14 0.41
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (40 bp):
TACTGCATATCTGATACTGTACTAAGATGGACTAAGGCCC
Found at i:41081309 original size:27 final size:27
Alignment explanation
Indices: 41081288--41081386 Score: 139
Period size: 27 Copynumber: 3.7 Consensus size: 27
41081278 ATTCAGAGTT
41081288 CGCCACAAAGGT-TATTCTTTCATATTA
1 CGCCACAAAGGTGT-TTCTTTCATATTA
*
41081315 CGCCACAAAGGTGTTTCTTTTATATTA
1 CGCCACAAAGGTGTTTCTTTCATATTA
*
41081342 CGCCACAAAGGTGTTTCTTTTATATTA
1 CGCCACAAAGGTGTTTCTTTCATATTA
*
41081369 CAG-CACAAAGGTTTTTCT
1 C-GCCACAAAGGTGTTTCT
41081387 ATCCTGATGT
Statistics
Matches: 68, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
27 66 0.97
28 2 0.03
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.38
Consensus pattern (27 bp):
CGCCACAAAGGTGTTTCTTTCATATTA
Found at i:41084352 original size:15 final size:15
Alignment explanation
Indices: 41084340--41084384 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
41084330 ATTTTTAATT
41084340 TTTTTAATTTTAAAG
1 TTTTTAATTTTAAAG
* *
41084355 TTTTTATTTTTAAAAA
1 TTTTTAATTTT-AAAG
*
41084371 TTTTTATTTTTAAA
1 TTTTTAATTTTAAA
41084385 AATTATATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
15 13 0.48
16 14 0.52
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (15 bp):
TTTTTAATTTTAAAG
Found at i:41084385 original size:15 final size:15
Alignment explanation
Indices: 41084307--41084396 Score: 74
Period size: 15 Copynumber: 6.0 Consensus size: 15
41084297 TTTTGGAAAA
*
41084307 AAAATTTATATATTT
1 AAAATTTATATTTTT
*
41084322 AAAA-TGATATTTTT
1 AAAATTTATATTTTT
** * *
41084336 AATTTTTTTAATTTT
1 AAAATTTATATTTTT
* *
41084351 AAAGTTTTTATTTTT
1 AAAATTTATATTTTT
*
41084366 AAAAATTTTTATTTTT
1 -AAAATTTATATTTTT
*
41084382 AAAAATTATATTTTT
1 AAAATTTATATTTTT
41084397 CTGCTTTTCA
Statistics
Matches: 60, Mismatches: 13, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
14 10 0.17
15 36 0.60
16 14 0.23
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (15 bp):
AAAATTTATATTTTT
Found at i:41087008 original size:2 final size:2
Alignment explanation
Indices: 41087003--41087058 Score: 60
Period size: 2 Copynumber: 28.0 Consensus size: 2
41086993 ACACATTTCT
* * * *
41087003 TA TA TA GTA TA TA TA TA CA TA TT TC TT TA TA TA -A TA TA TA TA
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
41087045 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
41087059 ACTTTTATAA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
1 1 0.02
2 43 0.93
3 2 0.04
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:41087040 original size:27 final size:26
Alignment explanation
Indices: 41086983--41087051 Score: 84
Period size: 27 Copynumber: 2.6 Consensus size: 26
41086973 TACTATTTCT
* * *
41086983 ATATTTATACACACATTTCTTATATA
1 ATATATATATACATATTTCTTATATA
*
41087009 GTATATATATACATATTTCTTTATATA
1 ATATATATATACATATTTC-TTATATA
*
41087036 ATATATATATATATAT
1 ATATATATATACATAT
41087052 ATATATAACT
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
26 15 0.42
27 21 0.58
ACGTcount: A:0.41, C:0.09, G:0.01, T:0.49
Consensus pattern (26 bp):
ATATATATATACATATTTCTTATATA
Found at i:41088137 original size:5 final size:5
Alignment explanation
Indices: 41088127--41088153 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
41088117 GTGAGCATTC
41088127 AATCG AATCG AATCG AATCG AATCG AA
1 AATCG AATCG AATCG AATCG AATCG AA
41088154 AATTTTCGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.44, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
AATCG
Found at i:41088940 original size:30 final size:29
Alignment explanation
Indices: 41088906--41088962 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
41088896 AGGTGGGATG
*
41088906 GGAAGAGAATAAAAATTTTAGGGGAAAAGT
1 GGAAGAGAATAAAAATTTT-GGAGAAAAGT
* *
41088936 GGAAGGGAGTAAAAATTTTGGAGAAAA
1 GGAAGAGAATAAAAATTTTGGAGAAAA
41088963 ATAAAAGGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 7 0.29
30 17 0.71
ACGTcount: A:0.49, C:0.00, G:0.32, T:0.19
Consensus pattern (29 bp):
GGAAGAGAATAAAAATTTTGGAGAAAAGT
Found at i:41089191 original size:9 final size:9
Alignment explanation
Indices: 41089177--41089213 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
41089167 TATAGTTTGA
41089177 TATTCGAAT
1 TATTCGAAT
41089186 TATTCGAAT
1 TATTCGAAT
*
41089195 TATTCGAGT
1 TATTCGAAT
41089204 TATTCGAAT
1 TATTCGAAT
41089213 T
1 T
41089214 CGAAAGCTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:41089284 original size:9 final size:9
Alignment explanation
Indices: 41089267--41089297 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
41089257 TCGAGTTGAT
41089267 TCGAATAAC
1 TCGAATAAC
*
41089276 TCGATTAAC
1 TCGAATAAC
41089285 TCGAATAAC
1 TCGAATAAC
41089294 TCGA
1 TCGA
41089298 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:41091432 original size:31 final size:31
Alignment explanation
Indices: 41091394--41091487 Score: 125
Period size: 31 Copynumber: 3.0 Consensus size: 31
41091384 GTCAATCAAT
** *
41091394 TGATATATTCTTATGTATATTTTGTATGTTA
1 TGATATATTAGTATGTATATTATGTATGTTA
*
41091425 TGATATATTAGTATGTATATTATGTTTGTTA
1 TGATATATTAGTATGTATATTATGTATGTTA
* *
41091456 TGATATATTAGTGTGTATGTTATGATATGTTA
1 TGATATATTAGTATGTATATTATG-TATGTTA
41091488 GTATGTATAG
Statistics
Matches: 55, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
31 49 0.89
32 6 0.11
ACGTcount: A:0.28, C:0.01, G:0.17, T:0.54
Consensus pattern (31 bp):
TGATATATTAGTATGTATATTATGTATGTTA
Found at i:41091474 original size:17 final size:17
Alignment explanation
Indices: 41091417--41091474 Score: 52
Period size: 18 Copynumber: 3.5 Consensus size: 17
41091407 TGTATATTTT
41091417 GTATGTTATGATATATTA
1 GTATG-TATGATATATTA
41091435 GTATGTAT-AT-TA-T-
1 GTATGTATGATATATTA
*
41091448 GTTTGTTATGATATATTA
1 GTATG-TATGATATATTA
*
41091466 GTGTGTATG
1 GTATGTATG
41091475 TTATGATATG
Statistics
Matches: 33, Mismatches: 2, Indels: 11
0.72 0.04 0.24
Matches are distributed among these distances:
13 4 0.12
14 4 0.12
15 4 0.12
16 4 0.12
17 8 0.24
18 9 0.27
ACGTcount: A:0.28, C:0.00, G:0.21, T:0.52
Consensus pattern (17 bp):
GTATGTATGATATATTA
Done.