Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A05
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: 102776486
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2328156 characters in sequence are not A, C, G, or T
File 132 of 325
Found at i:41264001 original size:3 final size:3
Alignment explanation
Indices: 41263993--41264033 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
41263983 GAAATGTTGA
*
41263993 ATT ATT ATT ATT ATT ATT ATT ATT ACT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
41264034 AATATATGAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:41265524 original size:34 final size:35
Alignment explanation
Indices: 41265418--41265560 Score: 146
Period size: 35 Copynumber: 4.1 Consensus size: 35
41265408 ATGCCTTAAT
* *
41265418 TAAAGGCAACCTTAAAAAGGTTGGGATAGACCCGTC
1 TAAA-GCAATCTTAAAAAGGTTGGGATAGACACGTC
* *
41265454 T-AAGACAATCTTAAAAAGGTTGGGATATACTCGTC
1 TAAAG-CAATCTTAAAAAGGTTGGGATAGACACGTC
* * *
41265489 TAAAGTAATCTTAAAAA-GTTAGGATAGACAAGTC
1 TAAAGCAATCTTAAAAAGGTTGGGATAGACACGTC
* * * * *
41265523 TAAGGCAACCTCAAAAAGTTTGGGATAGACACATC
1 TAAAGCAATCTTAAAAAGGTTGGGATAGACACGTC
41265558 TAA
1 TAA
41265561 TAGGGTAGAT
Statistics
Matches: 88, Mismatches: 16, Indels: 7
0.79 0.14 0.06
Matches are distributed among these distances:
34 27 0.31
35 57 0.65
36 4 0.05
ACGTcount: A:0.41, C:0.15, G:0.20, T:0.24
Consensus pattern (35 bp):
TAAAGCAATCTTAAAAAGGTTGGGATAGACACGTC
Found at i:41265560 original size:69 final size:70
Alignment explanation
Indices: 41265428--41265560 Score: 169
Period size: 69 Copynumber: 1.9 Consensus size: 70
41265418 TAAAGGCAAC
* ** * * * * *
41265428 CTTAAAAAGGTTGGGATAGACCCGTCTAAGACAATCTTAAAAAGGTTGGGATATACTCGTCTAAA
1 CTTAAAAAGGTTAGGATAGACAAGTCTAAGACAACCTCAAAAAGGTTGGGATAGACACATCTAAA
41265493 GTAAT
66 GTAAT
* *
41265498 CTTAAAAA-GTTAGGATAGACAAGTCTAAGGCAACCTCAAAAAGTTTGGGATAGACACATCTAA
1 CTTAAAAAGGTTAGGATAGACAAGTCTAAGACAACCTCAAAAAGGTTGGGATAGACACATCTAA
41265561 TAGGGTAGAT
Statistics
Matches: 53, Mismatches: 10, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
69 45 0.85
70 8 0.15
ACGTcount: A:0.40, C:0.15, G:0.20, T:0.25
Consensus pattern (70 bp):
CTTAAAAAGGTTAGGATAGACAAGTCTAAGACAACCTCAAAAAGGTTGGGATAGACACATCTAAA
GTAAT
Found at i:41266818 original size:7 final size:7
Alignment explanation
Indices: 41266806--41266840 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
41266796 ATCTTGTCTT
41266806 CCATCCC
1 CCATCCC
41266813 CCAT-CC
1 CCATCCC
41266819 CCAT-CC
1 CCATCCC
41266825 CCATCCC
1 CCATCCC
41266832 CCATCCC
1 CCATCCC
41266839 CC
1 CC
41266841 TAATCTCTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 12 0.44
7 15 0.56
ACGTcount: A:0.14, C:0.71, G:0.00, T:0.14
Consensus pattern (7 bp):
CCATCCC
Found at i:41266822 original size:6 final size:6
Alignment explanation
Indices: 41266806--41266839 Score: 50
Period size: 6 Copynumber: 5.3 Consensus size: 6
41266796 ATCTTGTCTT
41266806 CCATCCC CCATCC CCATCC CCATCCC CCATCC CC
1 CCAT-CC CCATCC CCATCC CCAT-CC CCATCC CC
41266840 CTAATCTCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
6 16 0.62
7 10 0.38
ACGTcount: A:0.15, C:0.71, G:0.00, T:0.15
Consensus pattern (6 bp):
CCATCC
Found at i:41266824 original size:13 final size:14
Alignment explanation
Indices: 41266806--41266840 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
41266796 ATCTTGTCTT
41266806 CCATCCCCCAT-CC
1 CCATCCCCCATCCC
41266819 CCAT-CCCCATCCC
1 CCATCCCCCATCCC
41266832 CCATCCCCC
1 CCATCCCCC
41266841 TAATCTCTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 6 0.30
13 10 0.50
14 4 0.20
ACGTcount: A:0.14, C:0.71, G:0.00, T:0.14
Consensus pattern (14 bp):
CCATCCCCCATCCC
Found at i:41269002 original size:22 final size:22
Alignment explanation
Indices: 41268974--41269032 Score: 82
Period size: 22 Copynumber: 2.7 Consensus size: 22
41268964 TAAAGTTATC
* **
41268974 ATGTCTCAAGACAAATGGGTGT
1 ATGTCTCAAGACAAAAGGGCAT
41268996 ATGTCTCAAGACAAAAGGGCAT
1 ATGTCTCAAGACAAAAGGGCAT
*
41269018 ATTTCTCAAGACAAA
1 ATGTCTCAAGACAAA
41269033 GTCTAATATC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.39, C:0.17, G:0.20, T:0.24
Consensus pattern (22 bp):
ATGTCTCAAGACAAAAGGGCAT
Found at i:41270597 original size:3 final size:3
Alignment explanation
Indices: 41270589--41270836 Score: 61
Period size: 3 Copynumber: 84.0 Consensus size: 3
41270579 TTGGACATGT
* * * *
41270589 TTA TTA TTA TT- TTA ATA ATA TTA TTG TT- GTA TTCA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA
* * * * *
41270633 -TA TGTGA CTA TTA TGT- TCA TTA TTT TTA CTT- TTA TTA TTC TTT TTA
1 TTA T-T-A TTA TTA T-TA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA
** * * * * * *
41270679 TTA AGA TTA TTT TTA CTA TTA TT- TTT TTA -TA CTA TAA TTA TTC TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * ** * * *
41270725 TTA ATA -TA TTA TT- TTC TCC CTA TTA TTA TTA -TA TCA TTA TTA TTC
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * *
41270770 TTA TTGA TGTA TTA TTA TTT TTA TTT TCTA CT- TTA ATA TTA TTA TT-
1 TTA TT-A T-TA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA
* * *
41270816 GTA TTA TCA CTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA
41270837 CCATATCATT
Statistics
Matches: 173, Mismatches: 52, Indels: 40
0.65 0.20 0.15
Matches are distributed among these distances:
2 19 0.11
3 139 0.80
4 13 0.08
5 2 0.01
ACGTcount: A:0.28, C:0.07, G:0.04, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:41270765 original size:17 final size:17
Alignment explanation
Indices: 41270745--41270788 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
41270735 ATTTTCTCCC
41270745 TATTATTATTATATCAT-
1 TATTATTATTAT-TCATG
* *
41270762 TATTATTCTTATTGATG
1 TATTATTATTATTCATG
41270779 TATTATTATT
1 TATTATTATT
41270789 TTTATTTTCT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 3 0.13
17 20 0.87
ACGTcount: A:0.30, C:0.05, G:0.05, T:0.61
Consensus pattern (17 bp):
TATTATTATTATTCATG
Found at i:41270768 original size:20 final size:20
Alignment explanation
Indices: 41270745--41270847 Score: 64
Period size: 20 Copynumber: 5.0 Consensus size: 20
41270735 ATTTTCTCCC
41270745 TATTATTATTATATCATTAT
1 TATTATTATTATATCATTAT
* *
41270765 TATTCTTATTGATGT-ATTAT
1 TATTATTATT-ATATCATTAT
* * * * *
41270785 TATTTTTATTTTCTACTTTAA
1 TATTATTATTATAT-CATTAT
*
41270806 TATTATTATTGTATTATCACTAT
1 TATTATTA-T-TA-TATCATTAT
**
41270829 TATTATTACCATATCATTA
1 TATTATTATTATATCATTA
41270848 ATCTAATTAA
Statistics
Matches: 61, Mismatches: 16, Indels: 12
0.69 0.18 0.13
Matches are distributed among these distances:
19 2 0.03
20 30 0.49
21 14 0.23
22 1 0.02
23 12 0.20
24 2 0.03
ACGTcount: A:0.30, C:0.09, G:0.03, T:0.58
Consensus pattern (20 bp):
TATTATTATTATATCATTAT
Found at i:41275382 original size:30 final size:30
Alignment explanation
Indices: 41275334--41275410 Score: 102
Period size: 30 Copynumber: 2.6 Consensus size: 30
41275324 GGCCCCCTAA
*
41275334 TTGAAAATTTTTATTAAACCCTTAAAAGTT
1 TTGAAAATTTTAATTAAACCCTTAAAAGTT
***
41275364 TT-AAAAGTTTTAATTAAACCCTTAAGTTTT
1 TTGAAAA-TTTTAATTAAACCCTTAAAAGTT
41275394 TTGAAAATTTTAATTAA
1 TTGAAAATTTTAATTAA
41275411 GCCCCCTAGA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
29 4 0.10
30 33 0.80
31 4 0.10
ACGTcount: A:0.40, C:0.08, G:0.06, T:0.45
Consensus pattern (30 bp):
TTGAAAATTTTAATTAAACCCTTAAAAGTT
Found at i:41279606 original size:2 final size:2
Alignment explanation
Indices: 41279599--41279624 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
41279589 AATTTTATTT
41279599 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
41279625 AATAAGGTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:41283373 original size:21 final size:21
Alignment explanation
Indices: 41283347--41283387 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
41283337 ATCTGCTCAA
* *
41283347 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
41283368 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
41283388 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:41291268 original size:33 final size:33
Alignment explanation
Indices: 41291221--41291284 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
41291211 TGTGTACACT
**
41291221 TGAAAAGGTTAGGTATACTTTGTGTATACCATA
1 TGAAAAGGAAAGGTATACTTTGTGTATACCATA
*
41291254 TGAAAAGGAAAGGTATACTTTGTGTGTACCA
1 TGAAAAGGAAAGGTATACTTTGTGTATACCA
41291285 CTTGGAAAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.34, C:0.09, G:0.23, T:0.33
Consensus pattern (33 bp):
TGAAAAGGAAAGGTATACTTTGTGTATACCATA
Found at i:41295319 original size:18 final size:18
Alignment explanation
Indices: 41295308--41295342 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
41295298 TTATATTTTA
41295308 AAATAAAATTATTTATAT
1 AAATAAAATTATTTATAT
*
41295326 ACATAAAATTA-TTATAT
1 AAATAAAATTATTTATAT
41295343 TGTTTATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (18 bp):
AAATAAAATTATTTATAT
Found at i:41297608 original size:16 final size:16
Alignment explanation
Indices: 41297582--41297629 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
41297572 TAGTACATTT
41297582 TAATT-ATTTATATAA
1 TAATTAATTTATATAA
*
41297597 TAATTAATTTATATTA
1 TAATTAATTTATATAA
41297613 T-ATATAATTT-TATAA
1 TAAT-TAATTTATATAA
41297628 TA
1 TA
41297630 TAATATAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
15 12 0.43
16 16 0.57
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TAATTAATTTATATAA
Found at i:41297908 original size:20 final size:20
Alignment explanation
Indices: 41297881--41297923 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
41297871 TATTGAGTAT
41297881 ATTAAAAATGCTTTAATTATA
1 ATTAAAAA-GCTTTAATTATA
* *
41297902 ATTAAAAAGTTTTTATTATA
1 ATTAAAAAGCTTTAATTATA
41297922 AT
1 AT
41297924 ATTTGAGTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.47
Consensus pattern (20 bp):
ATTAAAAAGCTTTAATTATA
Found at i:41308259 original size:119 final size:120
Alignment explanation
Indices: 41308053--41308275 Score: 292
Period size: 119 Copynumber: 1.9 Consensus size: 120
41308043 TACTCGTTCA
*
41308053 AATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGAAT
1 AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGAAT
* *
41308118 TTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
66 ATAGTAACTAGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
* * ** *
41308173 AATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCCGG
1 AATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGA
* * *
41308235 ATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCCGGA
64 ATATAGTAAC-TAGCACAAATGCCTTCGGGACTTAACCCGGA
41308276 CATCATTCGA
Statistics
Matches: 89, Mismatches: 11, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
118 4 0.04
119 65 0.73
120 20 0.22
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (120 bp):
AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGAAT
ATAGTAACTAGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
Found at i:41308275 original size:40 final size:40
Alignment explanation
Indices: 41308032--41308275 Score: 282
Period size: 40 Copynumber: 6.1 Consensus size: 40
41308022 CGGAATTTAA
** *
41308032 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
41308072 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
41308112 CCGAATTTAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
41308152 CCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
41308191 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
41308231 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
41308271 CCGGA
1 CCGGA
41308276 CATCATTCGA
Statistics
Matches: 177, Mismatches: 20, Indels: 14
0.84 0.09 0.07
Matches are distributed among these distances:
38 2 0.01
39 32 0.18
40 131 0.74
41 12 0.07
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:41309466 original size:56 final size:56
Alignment explanation
Indices: 41309399--41309518 Score: 240
Period size: 56 Copynumber: 2.1 Consensus size: 56
41309389 TATTAGTTTA
41309399 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
41309455 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
41309511 TTGCCCAT
1 TTGCCCAT
41309519 CATCCCTTGT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 64 1.00
ACGTcount: A:0.23, C:0.24, G:0.09, T:0.44
Consensus pattern (56 bp):
TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
Found at i:41312768 original size:49 final size:49
Alignment explanation
Indices: 41312708--41313212 Score: 802
Period size: 49 Copynumber: 10.6 Consensus size: 49
41312698 GATAATTGTG
41312708 ATGTG-AA-TGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
41312755 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* *
41312804 ATGTGAAAGTG--TATATATGTGATAAGGCCGAATGGCCAATGTGATGA
1 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
41312851 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* *
41312900 ATGTGAAAGTG--TATATATGTGATAAGGCCGAATGGCCAATGTGATGA
1 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
41312947 ATGTGAAAGTGTATATATATGTGATAAGGCCT-ATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* *
41312995 ATGTGAAAGTG--TATATATGTGATAAGGCCGAATGGCCAATGTGATGA
1 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
41313042 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
41313091 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* * * * * * *
41313140 ATGTGAAAGTG--TATATATGTGACAGGGCCGAGTGGCCAACGTGATGG
1 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
41313187 ATGTGAAAGTGTATA-A-ATGTGATAAG
1 ATGTGAAAGTGTATATATATGTGATAAG
41313213 TCCGGAAGGG
Statistics
Matches: 426, Mismatches: 21, Indels: 22
0.91 0.04 0.05
Matches are distributed among these distances:
46 18 0.04
47 169 0.40
48 29 0.07
49 210 0.49
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.29
Consensus pattern (49 bp):
ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
Found at i:41312810 original size:96 final size:96
Alignment explanation
Indices: 41312708--41313212 Score: 845
Period size: 96 Copynumber: 5.3 Consensus size: 96
41312698 GATAATTGTG
* * * *
41312708 ATGTGAATGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATAT
1 ATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATAT
41312773 ATGTGATAAGGCCTAATGGCCGATGTGATGA
66 ATGTGATAAGGCCTAATGGCCGATGTGATGA
41312804 ATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATAT
1 ATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATAT
41312869 ATGTGATAAGGCCTAATGGCCGATGTGATGA
66 ATGTGATAAGGCCTAATGGCCGATGTGATGA
41312900 ATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATAT
1 ATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATAT
41312965 ATGTGATAAGGCCT-ATGGCCGATGTGATGA
66 ATGTGATAAGGCCTAATGGCCGATGTGATGA
41312995 ATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATAT
1 ATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATAT
41313060 ATGTGATAAGGCCTAATGGCCGATGTGATGA
66 ATGTGATAAGGCCTAATGGCCGATGTGATGA
* *
41313091 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TAT
1 ATGTGAAAGTG--TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATAT
* * * * * * *
41313154 ATATGTGACAGGGCCGAGTGGCCAACGTGATGG
64 ATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
41313187 ATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGAAAGTGTATATATGTGATAAG
41313213 TCCGGAAGGG
Statistics
Matches: 392, Mismatches: 14, Indels: 8
0.95 0.03 0.02
Matches are distributed among these distances:
94 14 0.04
95 95 0.24
96 238 0.61
98 45 0.11
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.29
Consensus pattern (96 bp):
ATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATAT
ATGTGATAAGGCCTAATGGCCGATGTGATGA
Found at i:41320863 original size:79 final size:79
Alignment explanation
Indices: 41320760--41320981 Score: 281
Period size: 79 Copynumber: 2.8 Consensus size: 79
41320750 GCTACTCGTT
* *
41320760 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGA
*
41320825 TTTAGTAACTCGCA
66 ATTAGTAACTCGCA
* *
41320839 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCACCAATGCCTTCGGG-CTTAGCCCG
1 CAAATGCCTTCGGGACTTAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCC-
*
41320902 GAATTAGTATCTCGCA
64 GAATTAGTAACTCGCA
* * * * *
41320918 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCC
1 CAAATGCCTTCGGGA-CTTAGCCCGGTTATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGCCC
41320981 G
64 G
41320982 GACATCATTC
Statistics
Matches: 124, Mismatches: 13, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
78 11 0.09
79 96 0.77
80 17 0.14
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (79 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGA
ATTAGTAACTCGCA
Found at i:41320983 original size:40 final size:40
Alignment explanation
Indices: 41320741--41320983 Score: 282
Period size: 40 Copynumber: 6.1 Consensus size: 40
41320731 CGGAATTTAA
** *
41320741 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
41320781 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
41320821 CC-GATTTAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
41320860 CCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
41320899 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
41320939 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
41320979 CCGGA
1 CCGGA
41320984 CATCATTCGA
Statistics
Matches: 177, Mismatches: 18, Indels: 16
0.84 0.09 0.08
Matches are distributed among these distances:
38 2 0.01
39 69 0.39
40 94 0.53
41 12 0.07
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:41322178 original size:56 final size:56
Alignment explanation
Indices: 41322111--41322230 Score: 231
Period size: 56 Copynumber: 2.1 Consensus size: 56
41322101 TATTAGTTTA
41322111 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
*
41322167 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
41322223 TTGCCCAT
1 TTGCCCAT
41322231 CATCCCTTGT
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 63 1.00
ACGTcount: A:0.23, C:0.23, G:0.09, T:0.45
Consensus pattern (56 bp):
TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
Found at i:41323360 original size:32 final size:32
Alignment explanation
Indices: 41323319--41323380 Score: 124
Period size: 32 Copynumber: 1.9 Consensus size: 32
41323309 TGGGGTTCGT
41323319 GGGTCCGTAACTGAACGACTTCGGCCCAATGG
1 GGGTCCGTAACTGAACGACTTCGGCCCAATGG
41323351 GGGTCCGTAACTGAACGACTTCGGCCCAAT
1 GGGTCCGTAACTGAACGACTTCGGCCCAAT
41323381 AGAGTTGAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.23, C:0.29, G:0.29, T:0.19
Consensus pattern (32 bp):
GGGTCCGTAACTGAACGACTTCGGCCCAATGG
Found at i:41340265 original size:41 final size:41
Alignment explanation
Indices: 41340205--41340287 Score: 157
Period size: 41 Copynumber: 2.0 Consensus size: 41
41340195 TATATAGGAC
41340205 TTAAATTAAAGTTTAGAAGACAATTGATTCAAACTTTTTTT
1 TTAAATTAAAGTTTAGAAGACAATTGATTCAAACTTTTTTT
*
41340246 TTAAATTAAAGTTTGGAAGACAATTGATTCAAACTTTTTTT
1 TTAAATTAAAGTTTAGAAGACAATTGATTCAAACTTTTTTT
41340287 T
1 T
41340288 CCTTATTTTC
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.37, C:0.07, G:0.11, T:0.45
Consensus pattern (41 bp):
TTAAATTAAAGTTTAGAAGACAATTGATTCAAACTTTTTTT
Found at i:41340380 original size:23 final size:23
Alignment explanation
Indices: 41340354--41340403 Score: 91
Period size: 23 Copynumber: 2.2 Consensus size: 23
41340344 ATGCAATATA
*
41340354 TGAATTAAAAGCATTTATTATGT
1 TGAAGTAAAAGCATTTATTATGT
41340377 TGAAGTAAAAGCATTTATTATGT
1 TGAAGTAAAAGCATTTATTATGT
41340400 TGAA
1 TGAA
41340404 AATAAAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.40, C:0.04, G:0.16, T:0.40
Consensus pattern (23 bp):
TGAAGTAAAAGCATTTATTATGT
Found at i:41351205 original size:5 final size:5
Alignment explanation
Indices: 41351195--41351220 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
41351185 ACACTAGAAC
41351195 TATTT TATTT TATTT TATTT TATTT T
1 TATTT TATTT TATTT TATTT TATTT T
41351221 TAATTAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TATTT
Found at i:41351839 original size:6 final size:6
Alignment explanation
Indices: 41351792--41351820 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
41351782 ACTTATTTCC
41351792 TTGTTT TTGTTT TTGTTT TTGTTT TTGTT
1 TTGTTT TTGTTT TTGTTT TTGTTT TTGTT
41351821 CATGTATATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (6 bp):
TTGTTT
Found at i:41356323 original size:19 final size:19
Alignment explanation
Indices: 41356317--41356353 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
41356307 TGAAAAAAAT
41356317 AGAAAAAACTAAAAAATAA
1 AGAAAAAACTAAAAAATAA
* *
41356336 AGAAAAAATTTAAAAATA
1 AGAAAAAACTAAAAAATA
41356354 TTTTTTTGGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.76, C:0.03, G:0.05, T:0.16
Consensus pattern (19 bp):
AGAAAAAACTAAAAAATAA
Found at i:41369759 original size:15 final size:17
Alignment explanation
Indices: 41369734--41369768 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
41369724 TAAAATATAT
41369734 AAAGTAAAT-AAAAGAA
1 AAAGTAAATAAAAAGAA
41369750 AAAG-AAATAAAAAGAA
1 AAAGTAAATAAAAAGAA
41369766 AAA
1 AAA
41369769 AAGCAAGGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.22
16 14 0.78
ACGTcount: A:0.80, C:0.00, G:0.11, T:0.09
Consensus pattern (17 bp):
AAAGTAAATAAAAAGAA
Found at i:41374018 original size:18 final size:18
Alignment explanation
Indices: 41373981--41374019 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
41373971 TTGGAAATCA
*
41373981 AAATTATTAAAAGATGAT
1 AAATTATTAAAAGATAAT
41373999 AAATTATTAAATAGA-AAT
1 AAATTATTAAA-AGATAAT
41374017 AAA
1 AAA
41374020 AATCATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 16 0.84
19 3 0.16
ACGTcount: A:0.62, C:0.00, G:0.08, T:0.31
Consensus pattern (18 bp):
AAATTATTAAAAGATAAT
Found at i:41374818 original size:7 final size:7
Alignment explanation
Indices: 41374808--41374834 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
41374798 GATAATGTCC
41374808 GATAAAT
1 GATAAAT
41374815 GATAAAT
1 GATAAAT
41374822 GATAAAT
1 GATAAAT
41374829 GATAAA
1 GATAAA
41374835 AATGTTACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.15, T:0.26
Consensus pattern (7 bp):
GATAAAT
Found at i:41375698 original size:60 final size:60
Alignment explanation
Indices: 41375625--41375746 Score: 235
Period size: 60 Copynumber: 2.0 Consensus size: 60
41375615 ATATAAGAGA
41375625 TGATTTATACATGTTAAGTGAATACATGTTATGGAAAGCATATGTGCATGGAAACTTAAT
1 TGATTTATACATGTTAAGTGAATACATGTTATGGAAAGCATATGTGCATGGAAACTTAAT
*
41375685 TGATTTATACATGTTAAGTGAATACATGTTATGGAAAGCATATGTGCATGGAAACTTGAT
1 TGATTTATACATGTTAAGTGAATACATGTTATGGAAAGCATATGTGCATGGAAACTTAAT
41375745 TG
1 TG
41375747 TTTGTTGAGC
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 61 1.00
ACGTcount: A:0.35, C:0.08, G:0.21, T:0.35
Consensus pattern (60 bp):
TGATTTATACATGTTAAGTGAATACATGTTATGGAAAGCATATGTGCATGGAAACTTAAT
Found at i:41379425 original size:43 final size:42
Alignment explanation
Indices: 41379358--41379577 Score: 221
Period size: 43 Copynumber: 5.1 Consensus size: 42
41379348 ATTTTGTACA
* * * *
41379358 ATGCCAACGTCCCTGACGT-GGTCTTACATGTAATCTCATACCG
1 ATGCCAACGTCCCAGA--TAGGTCTTACACGTAATCACATATCG
*** *
41379401 ATGCC-ACTGTCCCAGATAGAGTCTTACTTTTAAACACATATCG
1 ATGCCAAC-GTCCCAGATAG-GTCTTACACGTAATCACATATCG
*
41379444 ATGCCAACGTCCCAGACGT-GGTCTTAGACGTAATCACATATCG
1 ATGCCAACGTCCCAGA--TAGGTCTTACACGTAATCACATATCG
* *
41379487 ATGCCAACGTCCCAGACATGGTCTTAGACGTAATCACATATCG
1 ATGCCAACGTCCCAGATA-GGTCTTACACGTAATCACATATCG
* * *
41379530 ATGCCAACGTCCCAGACATGGTCTTACACGAAATCACATATCA
1 ATGCCAACGTCCCAGATA-GGTCTTACACGTAATCACATATCG
41379573 ATGCC
1 ATGCC
41379578 TCATATACAT
Statistics
Matches: 154, Mismatches: 15, Indels: 16
0.83 0.08 0.09
Matches are distributed among these distances:
41 1 0.01
42 3 0.02
43 146 0.95
44 3 0.02
45 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.25
Consensus pattern (42 bp):
ATGCCAACGTCCCAGATAGGTCTTACACGTAATCACATATCG
Found at i:41379511 original size:86 final size:86
Alignment explanation
Indices: 41379358--41379577 Score: 282
Period size: 86 Copynumber: 2.6 Consensus size: 86
41379348 ATTTTGTACA
* * * * *
41379358 ATGCCAACGTCCCTGACGTGGTCTTACATGTAATCTCATACCGATGCCACTGTCCCAGATAGAGT
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAATCACATATCGATGCCACTGTCCCAGACAGAGT
***
41379423 CTTACTTTTAAACACATATCG
66 CTTACACGTAAACACATATCG
*
41379444 ATGCCAACGTCCCAGACGTGGTCTTAGACGTAATCACATATCGATGCCAAC-GTCCCAGACATG-
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAATCACATATCGATGCC-ACTGTCCCAGACA-GA
* *
41379507 GTCTTAGACGTAATCACATATCG
64 GTCTTACACGTAAACACATATCG
* * *
41379530 ATGCCAACGTCCCAGACATGGTCTTACACGAAATCACATATCAATGCC
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAATCACATATCGATGCC
41379578 TCATATACAT
Statistics
Matches: 117, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
86 114 0.97
87 3 0.03
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.25
Consensus pattern (86 bp):
ATGCCAACGTCCCAGACGTGGTCTTACACGTAATCACATATCGATGCCACTGTCCCAGACAGAGT
CTTACACGTAAACACATATCG
Found at i:41380343 original size:15 final size:15
Alignment explanation
Indices: 41380320--41380350 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
41380310 TCAAAAATTC
41380320 CAATACAAAACATAT
1 CAATACAAAACATAT
*
41380335 CAATCCAAAACATAT
1 CAATACAAAACATAT
41380350 C
1 C
41380351 TTTCATATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.26, G:0.00, T:0.19
Consensus pattern (15 bp):
CAATACAAAACATAT
Found at i:41385049 original size:46 final size:46
Alignment explanation
Indices: 41384846--41385163 Score: 213
Period size: 46 Copynumber: 6.8 Consensus size: 46
41384836 ACTATCGAAA
* * * *
41384846 TCGAGGCCGACGCCATGTCCCAGACATGGTCTTATACTAGCTCTCACATAT
1 TCGAGGCCGATG-CATGTCCCAGACAT-GTCTTACACTGGCTCT--CAT-C
* * * *
41384897 TCG-TGCCGATGGTATGTCCCAGACATGGTCTTACACTAGCACCTCTAT-
1 TCGAGGCCGAT-GCATGTCCCAGACAT-GTCTTACACTGGC-TCTC-ATC
* * * * *
41384945 GCG-TGCCGATGCCATGTCCCAAACATGGTCTTACACT-G-ACACATC
1 TCGAGGCCGATG-CATGTCCCAGACAT-GTCTTACACTGGCTCTCATC
* *
41384990 TCGTA-GCCAATGCATGTCCTAGACATGTCTTACACTGGCT-TACATC
1 TCG-AGGCCGATGCATGTCCCAGACATGTCTTACACTGGCTCT-CATC
* *
41385036 TCGAGGCCGATGCATGTCCCAGACATGTCTTACACTAGCTCTCGTC
1 TCGAGGCCGATGCATGTCCCAGACATGTCTTACACTGGCTCTCATC
* * * * * *
41385082 TCAATGCCGA-CCATGTCCAAGACATGGTCTTGCACTGGCTCTCATAA
1 TCGAGGCCGATGCATGTCCCAGACAT-GTCTTACACTGGCTCTCAT-C
* *
41385129 T-GTGGTCGATGCATGTCCCAGACATGTCTTACACT
1 TCGAGGCCGATGCATGTCCCAGACATGTCTTACACT
41385164 AGCGCACAAA
Statistics
Matches: 217, Mismatches: 35, Indels: 35
0.76 0.12 0.12
Matches are distributed among these distances:
44 12 0.06
45 31 0.14
46 85 0.39
47 17 0.08
48 32 0.15
49 1 0.00
50 33 0.15
51 6 0.03
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.27
Consensus pattern (46 bp):
TCGAGGCCGATGCATGTCCCAGACATGTCTTACACTGGCTCTCATC
Found at i:41390764 original size:9 final size:9
Alignment explanation
Indices: 41390752--41390777 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
41390742 AGGAATCAGA
41390752 GGAGGTGGG
1 GGAGGTGGG
41390761 GGAGGTGGG
1 GGAGGTGGG
41390770 GGAGGTGG
1 GGAGGTGG
41390778 AGTGTTCGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.77, T:0.12
Consensus pattern (9 bp):
GGAGGTGGG
Found at i:41392733 original size:46 final size:45
Alignment explanation
Indices: 41392663--41392820 Score: 164
Period size: 46 Copynumber: 3.4 Consensus size: 45
41392653 CCTTGTCCCT
*
41392663 GACATGGTCTTACACTGAC--ACATCTCGTAGCCGATGCATGTCCTA
1 GACATGGTCTTACACTGGCTTACATCTCG-AGCCGATGCATGTCC-A
*
41392708 GACAT-GTCTTACACTGGCTTACATCTCGAGTCCGATACATGTCCAA
1 GACATGGTCTTACACTGGCTTACATCTCGAG-CCGATGCATGTCC-A
* * *
41392754 GACAT-GTCTTACACTAGCTCT-CATCTCAATGCCGATGCCATGTCGCG
1 GACATGGTCTTACACTGGCT-TACATCTCGA-GCCGATG-CATGTC-CA
41392801 GACATGGTCTTACACTGGCT
1 GACATGGTCTTACACTGGCT
41392821 CTCATAATTT
Statistics
Matches: 97, Mismatches: 8, Indels: 13
0.82 0.07 0.11
Matches are distributed among these distances:
44 12 0.12
45 7 0.07
46 51 0.53
47 13 0.13
48 14 0.14
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.28
Consensus pattern (45 bp):
GACATGGTCTTACACTGGCTTACATCTCGAGCCGATGCATGTCCA
Found at i:41395322 original size:5 final size:5
Alignment explanation
Indices: 41395312--41395417 Score: 144
Period size: 5 Copynumber: 21.2 Consensus size: 5
41395302 AAGTATAACT
* * * *
41395312 TATCA TATCA TAACA TAT-A GTATCA TACCA TA-CAA TACCA TATCA TACCA
1 TATCA TATCA TATCA TATCA -TATCA TATCA TATC-A TATCA TATCA TATCA
41395362 TATCA TATCA TATCA TATCA TATCA TATCA TATCA TATCA TATCA TATCA
1 TATCA TATCA TATCA TATCA TATCA TATCA TATCA TATCA TATCA TATCA
41395412 TATCA T
1 TATCA T
41395418 GTCCTAGCCC
Statistics
Matches: 91, Mismatches: 6, Indels: 8
0.87 0.06 0.08
Matches are distributed among these distances:
4 2 0.02
5 87 0.96
6 2 0.02
ACGTcount: A:0.42, C:0.22, G:0.01, T:0.36
Consensus pattern (5 bp):
TATCA
Found at i:41395989 original size:20 final size:19
Alignment explanation
Indices: 41395960--41395997 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
41395950 GTATAGAAAA
41395960 AGAAAAGGGAACAAAAGAG
1 AGAAAAGGGAACAAAAGAG
*
41395979 AGAACAAGGGAATAAAAGA
1 AGAA-AAGGGAACAAAAGA
41395998 TATGTGGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.63, C:0.05, G:0.29, T:0.03
Consensus pattern (19 bp):
AGAAAAGGGAACAAAAGAG
Found at i:41402718 original size:77 final size:77
Alignment explanation
Indices: 41402624--41402797 Score: 269
Period size: 77 Copynumber: 2.3 Consensus size: 77
41402614 CGACATAGTG
*
41402624 ATATCATGGCCTGAAGCCAAATCAG-CTGATATTCATGGCCCAAAGCCAAATCGGTATAACTCGC
1 ATATCATGGCCCGAAGCCAAATCAGCCT-ATATTCATGGCCCAAAGCCAAATCGGTATAACTCGC
* **
41402688 ATCCGAATTGCTA
65 ACCCGAAGAGCTA
* * *
41402701 ATATTATGTCCCGAAGCCAAATCAGCCTATATTCATGGCCCAAAGCCAAATCGGTATAACTTGCA
1 ATATCATGGCCCGAAGCCAAATCAGCCTATATTCATGGCCCAAAGCCAAATCGGTATAACTCGCA
41402766 CCCGAAGAGCTA
66 CCCGAAGAGCTA
41402778 ATATCATGGCCCGAAGCCAA
1 ATATCATGGCCCGAAGCCAA
41402798 CTCAATGTAT
Statistics
Matches: 87, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
77 85 0.98
78 2 0.02
ACGTcount: A:0.33, C:0.27, G:0.18, T:0.22
Consensus pattern (77 bp):
ATATCATGGCCCGAAGCCAAATCAGCCTATATTCATGGCCCAAAGCCAAATCGGTATAACTCGCA
CCCGAAGAGCTA
Found at i:41408686 original size:20 final size:22
Alignment explanation
Indices: 41408661--41408700 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
41408651 TGCTAGATAC
41408661 AGGGGC-ACA-GCCCGTGTGGG
1 AGGGGCAACACGCCCGTGTGGG
41408681 AGGGGCAACACGCCCGTGTG
1 AGGGGCAACACGCCCGTGTG
41408701 ACCAATTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.33
21 3 0.17
22 9 0.50
ACGTcount: A:0.17, C:0.28, G:0.45, T:0.10
Consensus pattern (22 bp):
AGGGGCAACACGCCCGTGTGGG
Found at i:41409332 original size:17 final size:17
Alignment explanation
Indices: 41409310--41409343 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
41409300 TACAAAATGA
41409310 GAGATTTATCCCAAGCC
1 GAGATTTATCCCAAGCC
41409327 GAGATTTATCCCAAGCC
1 GAGATTTATCCCAAGCC
41409344 AACACATTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.29, G:0.18, T:0.24
Consensus pattern (17 bp):
GAGATTTATCCCAAGCC
Found at i:41420691 original size:46 final size:45
Alignment explanation
Indices: 41420594--41420720 Score: 168
Period size: 46 Copynumber: 2.8 Consensus size: 45
41420584 TGGGGTAAGG
*
41420594 TGCCGATGCCATGTCCCAGACATGGTCTTACACTGACACATCTCG
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTGACACATCTCA
* *
41420639 TAGCCGATG-CATGTCCCAGACAT-GTCTTACACTAGCACTCGTCTCAA
1 T-GCCGATGCCATGTCCCAGACATGGTCTTACACT-G-ACACATCTC-A
*
41420686 TGCCGATGCCATGTCCCAAACATGGTCTTACACTG
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTG
41420721 GTTCTCATAA
Statistics
Matches: 72, Mismatches: 4, Indels: 10
0.84 0.05 0.12
Matches are distributed among these distances:
44 10 0.14
45 16 0.22
46 21 0.29
47 15 0.21
48 10 0.14
ACGTcount: A:0.24, C:0.32, G:0.19, T:0.25
Consensus pattern (45 bp):
TGCCGATGCCATGTCCCAGACATGGTCTTACACTGACACATCTCA
Found at i:41423820 original size:18 final size:20
Alignment explanation
Indices: 41423788--41423838 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 20
41423778 GTTAATTTCA
*
41423788 ATTTTTTAATATTATTTAAT
1 ATTTTTTAATATTATGTAAT
41423808 ATTTTTT-AT-TTATGTAAT
1 ATTTTTTAATATTATGTAAT
*
41423826 -TTTAATTAATATT
1 ATTT-TTTAATATT
41423839 TTTTTATACA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
17 3 0.12
18 10 0.38
19 4 0.15
20 9 0.35
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (20 bp):
ATTTTTTAATATTATGTAAT
Found at i:41425354 original size:18 final size:18
Alignment explanation
Indices: 41425331--41425366 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
41425321 TGCCAGGTGC
41425331 GTATCCTAGCCCTTATAT
1 GTATCCTAGCCCTTATAT
*
41425349 GTATCCTTGCCCTTATAT
1 GTATCCTAGCCCTTATAT
41425367 ATTTCCTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.19, C:0.28, G:0.11, T:0.42
Consensus pattern (18 bp):
GTATCCTAGCCCTTATAT
Found at i:41425373 original size:18 final size:18
Alignment explanation
Indices: 41425332--41425374 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
41425322 GCCAGGTGCG
* *
41425332 TATCCTAGCCCTTATATG
1 TATCCTTGCCCTTATATA
41425350 TATCCTTGCCCTTATATA
1 TATCCTTGCCCTTATATA
*
41425368 TTTCCTT
1 TATCCTT
41425375 TTCCTAGTCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.19, C:0.28, G:0.07, T:0.47
Consensus pattern (18 bp):
TATCCTTGCCCTTATATA
Found at i:41427872 original size:35 final size:35
Alignment explanation
Indices: 41427832--41427900 Score: 111
Period size: 35 Copynumber: 2.0 Consensus size: 35
41427822 AAGCACCGAG
41427832 AAAACCATTCTCACTAGAAAAATCCTTACAACTTA
1 AAAACCATTCTCACTAGAAAAATCCTTACAACTTA
* * *
41427867 AAAACCATTCTCACTGGAAAATTCCTTACTACTT
1 AAAACCATTCTCACTAGAAAAATCCTTACAACTT
41427901 TCAATTCACC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.41, C:0.26, G:0.04, T:0.29
Consensus pattern (35 bp):
AAAACCATTCTCACTAGAAAAATCCTTACAACTTA
Found at i:41428966 original size:25 final size:25
Alignment explanation
Indices: 41428938--41429009 Score: 126
Period size: 25 Copynumber: 2.9 Consensus size: 25
41428928 CAACTTATAC
* *
41428938 CTTCTCAACTTCTTCAATTTCTATT
1 CTTCTGAAATTCTTCAATTTCTATT
41428963 CTTCTGAAATTCTTCAATTTCTATT
1 CTTCTGAAATTCTTCAATTTCTATT
41428988 CTTCTGAAATTCTTCAATTTCT
1 CTTCTGAAATTCTTCAATTTCT
41429010 CTTGCTATAA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 45 1.00
ACGTcount: A:0.22, C:0.24, G:0.03, T:0.51
Consensus pattern (25 bp):
CTTCTGAAATTCTTCAATTTCTATT
Found at i:41429213 original size:28 final size:28
Alignment explanation
Indices: 41429160--41429214 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
41429150 ATTTTCAACC
* *
41429160 TATTTTTTCAGAACCGTCTTTTCAAAAT
1 TATTTTTTCAGAACCGTCTATACAAAAT
*
41429188 TATTTTTTCAGAATC-TACTATACAAAA
1 TATTTTTTCAGAACCGT-CTATACAAAA
41429215 AGAGCGTCCA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 1 0.04
28 22 0.96
ACGTcount: A:0.35, C:0.16, G:0.05, T:0.44
Consensus pattern (28 bp):
TATTTTTTCAGAACCGTCTATACAAAAT
Found at i:41429312 original size:126 final size:126
Alignment explanation
Indices: 41429082--41429379 Score: 499
Period size: 126 Copynumber: 2.4 Consensus size: 126
41429072 AGAGGTATTG
*
41429082 TACAAAAAGAGCGTCCAGCTGAGAGCTTTTTTCAGTACTTTTGCTGACAGTGCATCCTACTTGAA
1 TACAAAAAGAGCGTCCAGCTGAGAGCTTTTTTTAGTACTTTTGCTGACAGTGCATCCTACTTGAA
* ** *
41429147 GCGATTTTCAACCTATTTTTTCAGAACCGTCTTTTCAAAATTATTTTTTCAGAATCTACTA
66 GCGATTTTCAACCTATTTTTTCAGAACCATCTTCCCAAAAATATTTTTTCAGAATCTACTA
*
41429208 TACAAAAAGAGCGTCCAGCTAAGAGCTTTTTTTAGTACTTTTGCTGACAGTGCATCCTACTTGAA
1 TACAAAAAGAGCGTCCAGCTGAGAGCTTTTTTTAGTACTTTTGCTGACAGTGCATCCTACTTGAA
*
41429273 GC-ATTTTTCAACCTATTTTTTCAGAACCATCTTCCCAAAAATATTTTTTTAGAATCTACTA
66 GCGA-TTTTCAACCTATTTTTTCAGAACCATCTTCCCAAAAATATTTTTTCAGAATCTACTA
* *
41429334 TATAAAAAGAGCGTCCAACTGAGAGCTTTTTTTAGTACTTTTGCTG
1 TACAAAAAGAGCGTCCAGCTGAGAGCTTTTTTTAGTACTTTTGCTG
41429380 GCTGTACAAA
Statistics
Matches: 161, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
125 1 0.01
126 160 0.99
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (126 bp):
TACAAAAAGAGCGTCCAGCTGAGAGCTTTTTTTAGTACTTTTGCTGACAGTGCATCCTACTTGAA
GCGATTTTCAACCTATTTTTTCAGAACCATCTTCCCAAAAATATTTTTTCAGAATCTACTA
Found at i:41432077 original size:13 final size:13
Alignment explanation
Indices: 41432059--41432083 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41432049 TAATTTATAT
41432059 GTGTGAAAATTTC
1 GTGTGAAAATTTC
41432072 GTGTGAAAATTT
1 GTGTGAAAATTT
41432084 TATCGTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:41433307 original size:43 final size:43
Alignment explanation
Indices: 41433186--41433342 Score: 189
Period size: 43 Copynumber: 3.7 Consensus size: 43
41433176 TGTGTTATCA
* *
41433186 TGTAAGACCACGTCTGGGAAGTTGGCATTG-ACTTATGATTTACG
1 TGTAAGACCACGTCTGGGACGTTGGCATCGTA-TT-TGATTTACG
*
41433230 TATAAGACCACGTCTGGGACGTTGGCATCGTATTTGATTT-CG
1 TGTAAGACCACGTCTGGGACGTTGGCATCGTATTTGATTTACG
* *
41433272 TGTAAGACC-CTGTTTGGGACAG-TGGCATCGATATTTG-TTTACA
1 TGTAAGACCAC-GTCTGGGAC-GTTGGCATCG-TATTTGATTTACG
41433315 TGTAAGACCACGTCTGGGACGTTGGCAT
1 TGTAAGACCACGTCTGGGACGTTGGCAT
41433343 TGTGCGAGCT
Statistics
Matches: 99, Mismatches: 7, Indels: 15
0.82 0.06 0.12
Matches are distributed among these distances:
41 1 0.01
42 30 0.30
43 37 0.37
44 30 0.30
45 1 0.01
ACGTcount: A:0.23, C:0.18, G:0.27, T:0.32
Consensus pattern (43 bp):
TGTAAGACCACGTCTGGGACGTTGGCATCGTATTTGATTTACG
Found at i:41446710 original size:36 final size:36
Alignment explanation
Indices: 41446670--41446954 Score: 173
Period size: 36 Copynumber: 7.7 Consensus size: 36
41446660 TAACTCTCAA
* * *
41446670 AATTATTCAATAACAGTCAGTTATTCGGTAACAATC
1 AATTATTCAGTAACAATCAGTTATTCAGTAACAATC
* * * * *
41446706 AATTATTCAATAATAACCAGTTATTCAATATCGATCAATT
1 AATTATTCAGTAACAATCAGTTATTCAGTA---A-CAATC
* * *
41446746 AATTGGTTATCTAGTAACAGTCAATTATTCAGTAA-AATC
1 AATT--AT-TC-AGTAACAATCAGTTATTCAGTAACAATC
* * * **
41446785 AGA-TATTTAGTAACAATTAAGTTATTCAGTAGCTGTC
1 A-ATTATTCAGTAACAA-TCAGTTATTCAGTAACAATC
* **
41446822 -ATTCATTCAGTGACAATCAGTTATTCAGTAGTAATC
1 AATT-ATTCAGTAACAATCAGTTATTCAGTAACAATC
* * *
41446858 AATTATTCAGTAATATTCAGTTATTCAGTAACAGTC
1 AATTATTCAGTAACAATCAGTTATTCAGTAACAATC
* * * * * *
41446894 TAA-TATCCAGTAACAGTCAATTATCCGGTAACAGTC
1 -AATTATTCAGTAACAATCAGTTATTCAGTAACAATC
*
41446930 AATTATTCAGTAATAATCAGTTATT
1 AATTATTCAGTAACAATCAGTTATT
41446955 TTATACCTTT
Statistics
Matches: 188, Mismatches: 45, Indels: 32
0.71 0.17 0.12
Matches are distributed among these distances:
35 10 0.05
36 125 0.66
37 18 0.10
39 6 0.03
40 9 0.05
41 1 0.01
42 1 0.01
43 2 0.01
44 16 0.09
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.36
Consensus pattern (36 bp):
AATTATTCAGTAACAATCAGTTATTCAGTAACAATC
Found at i:41446779 original size:18 final size:18
Alignment explanation
Indices: 41446758--41446942 Score: 144
Period size: 18 Copynumber: 10.3 Consensus size: 18
41446748 TTGGTTATCT
41446758 AGTAACAGTCAATTATTC
1 AGTAACAGTCAATTATTC
* *
41446776 AGTAA-AATCAGA-TATTT
1 AGTAACAGTCA-ATTATTC
* *
41446793 AGTAACAATTAAGTTATTC
1 AGTAACAGTCAA-TTATTC
* *
41446812 AGTAGCTGTC-ATTCATTC
1 AGTAACAGTCAATT-ATTC
* * *
41446830 AGTGACAATCAGTTATTC
1 AGTAACAGTCAATTATTC
** *
41446848 AGTAGTAATCAATTATTC
1 AGTAACAGTCAATTATTC
* * *
41446866 AGTAATATTCAGTTATTC
1 AGTAACAGTCAATTATTC
*
41446884 AGTAACAGTCTAA-TATCC
1 AGTAACAGTC-AATTATTC
*
41446902 AGTAACAGTCAATTATCC
1 AGTAACAGTCAATTATTC
*
41446920 GGTAACAGTCAATTATTC
1 AGTAACAGTCAATTATTC
41446938 AGTAA
1 AGTAA
41446943 TAATCAGTTA
Statistics
Matches: 132, Mismatches: 27, Indels: 16
0.75 0.15 0.09
Matches are distributed among these distances:
17 18 0.14
18 101 0.77
19 13 0.10
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.35
Consensus pattern (18 bp):
AGTAACAGTCAATTATTC
Found at i:41446887 original size:72 final size:71
Alignment explanation
Indices: 41446753--41446954 Score: 192
Period size: 72 Copynumber: 2.8 Consensus size: 71
41446743 ATTAATTGGT
* * * * * *
41446753 TATCTAGTAACAGTCAATTATTCAGTAAAATCAGA-TATTTAGTAACAATTAAGTTATTCAGTAG
1 TATCCAGTAACAATCAATTATTCAGTAAAATCA-ATTATTCAGTAA-TATTCAGTTATTCAGTAA
* *
41446817 CTGTC-AT
64 CAGTCTAA
* * * *
41446824 TCATTCAGTGACAATCAGTTATTCAGTAGTAATCAATTATTCAGTAATATTCAGTTATTCAGTAA
1 T-ATCCAGTAACAATCAATTATTCAGTA-AAATCAATTATTCAGTAATATTCAGTTATTCAGTAA
41446889 CAGTCTAA
64 CAGTCTAA
* * * * *
41446897 TATCCAGTAACAGTCAATTATCCGGTAACAGTCAATTATTCAGTAATAATCAGTTATT
1 TATCCAGTAACAATCAATTATTCAGTAA-AATCAATTATTCAGTAATATTCAGTTATT
41446955 TTATACCTTT
Statistics
Matches: 105, Mismatches: 21, Indels: 9
0.78 0.16 0.07
Matches are distributed among these distances:
71 1 0.01
72 88 0.84
73 16 0.15
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.36
Consensus pattern (71 bp):
TATCCAGTAACAATCAATTATTCAGTAAAATCAATTATTCAGTAATATTCAGTTATTCAGTAACA
GTCTAA
Found at i:41446953 original size:18 final size:18
Alignment explanation
Indices: 41446672--41446954 Score: 133
Period size: 18 Copynumber: 15.3 Consensus size: 18
41446662 ACTCTCAAAA
* *
41446672 TTATTCAATAACAGTCAG
1 TTATTCAGTAACAATCAG
* *
41446690 TTATTCGGTAACAATCAA
1 TTATTCAGTAACAATCAG
* * *
41446708 TTATTCAATAATAACCAG
1 TTATTCAGTAACAATCAG
* *
41446726 TTATTCAATATCGATCAATTAATTGG
1 TTATTCAGTA---A-CAA-TCA---G
* *
41446752 TTA-TCTAGTAACAGTCAA
1 TTATTC-AGTAACAATCAG
41446770 TTATTCAGTAA-AATCAG
1 TTATTCAGTAACAATCAG
* * *
41446787 ATATTTAGTAACAATTAAG
1 TTATTCAGTAACAA-TCAG
* **
41446806 TTATTCAGTAGCTGTCA-
1 TTATTCAGTAACAATCAG
*
41446823 TTCATTCAGTGACAATCAG
1 TT-ATTCAGTAACAATCAG
** *
41446842 TTATTCAGTAGTAATCAA
1 TTATTCAGTAACAATCAG
* *
41446860 TTATTCAGTAATATTCAG
1 TTATTCAGTAACAATCAG
*
41446878 TTATTCAGTAACAGTCTA-
1 TTATTCAGTAACAATC-AG
* * * *
41446896 ATATCCAGTAACAGTCAA
1 TTATTCAGTAACAATCAG
* * * *
41446914 TTATCCGGTAACAGTCAA
1 TTATTCAGTAACAATCAG
*
41446932 TTATTCAGTAATAATCAG
1 TTATTCAGTAACAATCAG
41446950 TTATT
1 TTATT
41446955 TTATACCTTT
Statistics
Matches: 200, Mismatches: 49, Indels: 32
0.71 0.17 0.11
Matches are distributed among these distances:
17 16 0.08
18 149 0.75
19 17 0.09
21 3 0.01
22 4 0.02
23 2 0.01
25 2 0.01
26 7 0.04
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.36
Consensus pattern (18 bp):
TTATTCAGTAACAATCAG
Found at i:41447130 original size:47 final size:47
Alignment explanation
Indices: 41447071--41447187 Score: 164
Period size: 47 Copynumber: 2.5 Consensus size: 47
41447061 CAGTAACAGT
* * *
41447071 AACAGTAGCAGTATGGTACACAGAATACCTCATCGGAACAAATCCGG
1 AACAGTAACAGTACGGTACACAGAATACCTCATCGGAACAAATCCGA
* * *
41447118 GACAGTAACAGTACGGTACACAGAGTACCTCATCGGAACAAATCTGA
1 AACAGTAACAGTACGGTACACAGAATACCTCATCGGAACAAATCCGA
41447165 AACAGTAACAGTAACGGTA-ACAG
1 AACAGTAACAGT-ACGGTACACAG
41447188 TATTCAACAC
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
47 56 0.90
48 6 0.10
ACGTcount: A:0.40, C:0.22, G:0.21, T:0.16
Consensus pattern (47 bp):
AACAGTAACAGTACGGTACACAGAATACCTCATCGGAACAAATCCGA
Found at i:41447232 original size:45 final size:45
Alignment explanation
Indices: 41447170--41447279 Score: 148
Period size: 45 Copynumber: 2.4 Consensus size: 45
41447160 TCTGAAACAG
* *
41447170 TAACAGTAACGGTAACAGTATTCAACACACAAAGTGCTAAATCGA
1 TAACAGTAACAGTAACAGTATTCAACACACAAAGTGCCAAATCGA
* * * * *
41447215 TAACGGTAATAGTAACAGTATTCGACACACAAAGTGCCGAATCGG
1 TAACAGTAACAGTAACAGTATTCAACACACAAAGTGCCAAATCGA
*
41447260 TAACAGTAACGGTAACAGTA
1 TAACAGTAACAGTAACAGTA
41447280 ACAGTAGTCG
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 55 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.20
Consensus pattern (45 bp):
TAACAGTAACAGTAACAGTATTCAACACACAAAGTGCCAAATCGA
Found at i:41447270 original size:51 final size:49
Alignment explanation
Indices: 41447156--41447294 Score: 142
Period size: 45 Copynumber: 2.8 Consensus size: 49
41447146 CTCATCGGAA
* * *
41447156 CAAATCTGAAACAGTAACAGTAACGGTAACAGTATTCAACACACAAAGTGC
1 CAAATC-G-AACAGTAACGGTAACAGTAACAGTATTCGACACACAAAGTGC
* *
41447207 TAAATCG---A-TAACGGTAATAGTAACAGTATTCGACACACAAAGTGC
1 CAAATCGAACAGTAACGGTAACAGTAACAGTATTCGACACACAAAGTGC
* * *
41447252 CGAATCGGTAACAGTAACGGTAACAGTAACAGTAGTCGGCACA
1 CAAATC-G-AACAGTAACGGTAACAGTAACAGTATTCGACACA
41447295 TAAGTTCCTG
Statistics
Matches: 72, Mismatches: 10, Indels: 12
0.77 0.11 0.13
Matches are distributed among these distances:
45 37 0.51
46 2 0.03
50 2 0.03
51 31 0.43
ACGTcount: A:0.42, C:0.20, G:0.19, T:0.19
Consensus pattern (49 bp):
CAAATCGAACAGTAACGGTAACAGTAACAGTATTCGACACACAAAGTGC
Found at i:41447274 original size:12 final size:12
Alignment explanation
Indices: 41447257--41447281 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
41447247 AGTGCCGAAT
41447257 CGGTAACAGTAA
1 CGGTAACAGTAA
41447269 CGGTAACAGTAA
1 CGGTAACAGTAA
41447281 C
1 C
41447282 AGTAGTCGGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.20, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTAACAGTAA
Found at i:41448821 original size:20 final size:18
Alignment explanation
Indices: 41448787--41448831 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 18
41448777 AAACTTTCAA
41448787 TTTTCCCTTTCTTCTTTC
1 TTTTCCCTTTCTTCTTTC
41448805 TTTTCTCCTTTCTTTCTTTC
1 TTTTC-CCTTTC-TTCTTTC
41448825 -TTTCCCT
1 TTTTCCCT
41448832 GCTTTTCATT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 8 0.32
19 10 0.40
20 7 0.28
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTTCCCTTTCTTCTTTC
Found at i:41457459 original size:87 final size:87
Alignment explanation
Indices: 41457266--41457487 Score: 232
Period size: 87 Copynumber: 2.5 Consensus size: 87
41457256 TTAATGGTGT
* ** * * *
41457266 AAAAAACCCTTAAATTTTTTCAAAAACTTCAATTAAGCCCCTACTTTTTTTGCATTCACTTGAGT
1 AAAAAACCCTCAAATTTTTTCAAAAA-AACAATTAAGCCCCTGCTTTTTTTGCACTCAATTGAGT
41457331 ACTTAAACTTGCACAATACATCA
65 ACTTAAACTTGCACAATACATCA
** * * * ** *
41457354 AAAGGACCGTCAATTTTTTTCAAAAAAAAAATTAAGCCCCTGCTTTTTTTTTACTCAATTGGGTA
1 AAAAAACCCTCAAATTTTTTCAAAAAAACAATTAAGCCCCTGCTTTTTTTGCACTCAATTGAGTA
* *
41457419 CTTAAACTTTCA-AATTGCAT-A
66 CTTAAACTTGCACAA-TACATCA
* * *
41457440 AAAAAACCCTCAAACTTTTTCAAAAAAAGCAACTAAGTCCCTGCTTTT
1 AAAAAACCCTCAAATTTTTTCAAAAAAA-CAATTAAGCCCCTGCTTTT
41457488 CCTTCTTTTT
Statistics
Matches: 108, Mismatches: 24, Indels: 5
0.79 0.18 0.04
Matches are distributed among these distances:
86 26 0.24
87 61 0.56
88 21 0.19
ACGTcount: A:0.37, C:0.21, G:0.08, T:0.34
Consensus pattern (87 bp):
AAAAAACCCTCAAATTTTTTCAAAAAAACAATTAAGCCCCTGCTTTTTTTGCACTCAATTGAGTA
CTTAAACTTGCACAATACATCA
Found at i:41457636 original size:19 final size:18
Alignment explanation
Indices: 41457614--41457672 Score: 57
Period size: 19 Copynumber: 3.2 Consensus size: 18
41457604 AAATCAATAA
*
41457614 AAAATATTAAATTTTAAT
1 AAAATATTAAATATTAAT
*
41457632 GAAAATATAAAAATATTAAT
1 -AAAATAT-TAAATATTAAT
* *
41457652 AAATTATTAAAAATT-AT
1 AAAATATTAAATATTAAT
41457669 AAAA
1 AAAA
41457673 ATTCAAAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
17 5 0.15
18 6 0.18
19 13 0.39
20 9 0.27
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.36
Consensus pattern (18 bp):
AAAATATTAAATATTAAT
Found at i:41457645 original size:20 final size:20
Alignment explanation
Indices: 41457614--41457666 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
41457604 AAATCAATAA
41457614 AAAATATT--AAATTTTAAT
1 AAAATATTAAAAATTTTAAT
*
41457632 GAAAATA-TAAAAATATTAAT
1 -AAAATATTAAAAATTTTAAT
*
41457652 AAATTATTAAAAATT
1 AAAATATTAAAAATT
41457667 ATAAAAATTC
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
18 1 0.04
19 11 0.39
20 16 0.57
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (20 bp):
AAAATATTAAAAATTTTAAT
Found at i:41457665 original size:10 final size:10
Alignment explanation
Indices: 41457639--41457675 Score: 51
Period size: 9 Copynumber: 3.8 Consensus size: 10
41457629 AATGAAAATA
41457639 TAAAAA-TAT
1 TAAAAATTAT
41457648 TAATAAATTAT
1 TAA-AAATTAT
41457659 TAAAAATTA-
1 TAAAAATTAT
41457668 TAAAAATT
1 TAAAAATT
41457676 CAAAAAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
9 11 0.42
10 9 0.35
11 6 0.23
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (10 bp):
TAAAAATTAT
Found at i:41457703 original size:31 final size:32
Alignment explanation
Indices: 41457665--41457770 Score: 92
Period size: 31 Copynumber: 3.2 Consensus size: 32
41457655 TTATTAAAAA
41457665 TTATAAAAATTC-AAAAAAAAATC-ATAAAATT
1 TTATAAAAA-TCGAAAAAAAAATCTATAAAATT
*
41457696 TTATAAAAATCGTAAAAAAAATCTATAAAA-T
1 TTATAAAAATCGAAAAAAAAATCTATAAAATT
* * **
41457727 ATATAGAAATATAGAAATACAGAAAAAATATAAAATT
1 TTATA-AAA-ATCGAAA-A-A-AAAATCTATAAAATT
41457764 TTATAAA
1 TTATAAA
41457771 GTTGTAAGAA
Statistics
Matches: 60, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
30 2 0.03
31 24 0.40
32 9 0.15
33 5 0.08
34 1 0.02
35 1 0.02
36 13 0.22
37 5 0.08
ACGTcount: A:0.63, C:0.05, G:0.04, T:0.28
Consensus pattern (32 bp):
TTATAAAAATCGAAAAAAAAATCTATAAAATT
Found at i:41457705 original size:68 final size:69
Alignment explanation
Indices: 41457593--41457770 Score: 181
Period size: 68 Copynumber: 2.6 Consensus size: 69
41457583 TAAATATTTG
* * * *
41457593 ATAAAAA-ATAAAAA-TCAATAAAAAATATTAAATTTTAATGAAAAT-AT-AAAAATAT-TAATA
1 ATAAAAATATAAAAATTCAAAAAAAAATATAAAATTTT-ATAAAAATCATAAAAAAAATCT-ATA
*
41457653 AATTAT
64 AAATAT
*
41457659 -TAAAAATTATAAAAATTCAAAAAAAAATCATAAAATTTTATAAAAATCGTAAAAAAAATCTATA
1 ATAAAAA-TATAAAAATTCAAAAAAAAAT-ATAAAATTTTATAAAAATCATAAAAAAAATCTATA
41457723 AAATAT
64 AAATAT
* * * *
41457729 ATAGAAATATAGAAATAC-AGAAAAAATATAAAATTTTATAAA
1 ATAAAAATATAAAAATTCAAAAAAAAATATAAAATTTTATAAA
41457771 GTTGTAAGAA
Statistics
Matches: 94, Mismatches: 10, Indels: 14
0.80 0.08 0.12
Matches are distributed among these distances:
65 6 0.06
67 7 0.07
68 33 0.35
69 18 0.19
70 24 0.26
71 6 0.06
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (69 bp):
ATAAAAATATAAAAATTCAAAAAAAAATATAAAATTTTATAAAAATCATAAAAAAAATCTATAAA
ATAT
Found at i:41457828 original size:67 final size:68
Alignment explanation
Indices: 41457680--41457810 Score: 176
Period size: 67 Copynumber: 1.9 Consensus size: 68
41457670 AAAATTCAAA
* * *
41457680 AAAAAATCATAAAATTTTATAAAAATCGTAAAAAAAATCTATAAAATATATAGAAATATAGAAAT
1 AAAAAAT-ATAAAATTTTATAAAAATCGTAAAAAAAATATAAAAAATATAAAGAAATATAGAAAT
41457745 ACAG
65 ACAG
* * * *
41457749 AAAAAATATAAAATTTTAT-AAAGTTGTAAGAAAATTATAAAAAATATAAAGAAATATA-AAAT
1 AAAAAATATAAAATTTTATAAAAATCGTAAAAAAAATATAAAAAATATAAAGAAATATAGAAAT
41457811 TCGTAAAGAA
Statistics
Matches: 55, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
66 4 0.07
67 32 0.58
68 12 0.22
69 7 0.13
ACGTcount: A:0.63, C:0.03, G:0.06, T:0.27
Consensus pattern (68 bp):
AAAAAATATAAAATTTTATAAAAATCGTAAAAAAAATATAAAAAATATAAAGAAATATAGAAATA
CAG
Found at i:41458025 original size:10 final size:10
Alignment explanation
Indices: 41458012--41458124 Score: 58
Period size: 9 Copynumber: 11.6 Consensus size: 10
41458002 TTTTGATACA
41458012 TTTTATAATT
1 TTTTATAATT
*
41458022 TTTTATGA-T
1 TTTTATAATT
* **
41458031 TTGTATAAAA
1 TTTTATAATT
* *
41458041 TTTTACAATA
1 TTTTATAATT
*
41458051 CTTTATAA-T
1 TTTTATAATT
**
41458060 TTTTACGA-T
1 TTTTATAATT
41458069 TTTTATAAATT
1 TTTTAT-AATT
*
41458080 TGTTTCTAATT
1 T-TTTATAATT
*
41458091 TTTTAATAA-A
1 TTTT-ATAATT
41458101 TTTTA-AATT
1 TTTTATAATT
41458110 TTTTAT-ATT
1 TTTTATAATT
41458119 TTTTAT
1 TTTTAT
41458125 TAAAATTTTA
Statistics
Matches: 77, Mismatches: 19, Indels: 15
0.69 0.17 0.14
Matches are distributed among these distances:
8 2 0.03
9 33 0.43
10 28 0.36
11 10 0.13
12 4 0.05
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.61
Consensus pattern (10 bp):
TTTTATAATT
Found at i:41458079 original size:19 final size:19
Alignment explanation
Indices: 41458012--41458080 Score: 68
Period size: 19 Copynumber: 3.6 Consensus size: 19
41458002 TTTTGATACA
* *
41458012 TTTTATAATTTTTTATGAT
1 TTTTATAAATTTTTACGAT
* * *
41458031 TTGTATAAAATTTTACAAT
1 TTTTATAAATTTTTACGAT
*
41458050 ACTTTAT-AATTTTTACGAT
1 -TTTTATAAATTTTTACGAT
41458069 TTTTATAAATTT
1 TTTTATAAATTT
41458081 GTTTCTAATT
Statistics
Matches: 38, Mismatches: 10, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
18 5 0.13
19 29 0.76
20 4 0.11
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.58
Consensus pattern (19 bp):
TTTTATAAATTTTTACGAT
Found at i:41458127 original size:21 final size:22
Alignment explanation
Indices: 41458103--41458155 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
41458093 TTAATAAATT
41458103 TTAAATTTTTTATATTT-TTTA
1 TTAAATTTTTTATATTTATTTA
* *
41458124 TTAAA-ATTTTATTTTTATTTA
1 TTAAATTTTTTATATTTATTTA
*
41458145 TTATATTTTTT
1 TTAAATTTTTT
41458156 GCCACATGTC
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 9 0.35
21 13 0.50
22 4 0.15
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (22 bp):
TTAAATTTTTTATATTTATTTA
Found at i:41458131 original size:29 final size:30
Alignment explanation
Indices: 41458074--41458134 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 30
41458064 ACGATTTTTA
*
41458074 TAAATTTGTTTCTAATTTTTTAATAAATTT
1 TAAATTTGTTTATAATTTTTTAATAAATTT
*
41458104 TAAATTT-TTTAT-ATTTTTTATTAAAATTT
1 TAAATTTGTTTATAATTTTTTAAT-AAATTT
41458133 TA
1 TA
41458135 TTTTTATTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 9 0.32
29 12 0.43
30 7 0.25
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (30 bp):
TAAATTTGTTTATAATTTTTTAATAAATTT
Found at i:41458411 original size:90 final size:89
Alignment explanation
Indices: 41458258--41458529 Score: 327
Period size: 88 Copynumber: 3.1 Consensus size: 89
41458248 GTCAAATAGC
* ** *
41458258 CTTTTTAATGCA-TTTTACAA-TTCAAGTACCTAATTGAGTGTTAAAAAAAATCAAGGGCTTAAT
1 CTTTTTAATGCATTTTTA-AAGTTCAAGTACCCAATTGAGTGAAAAAAAAAAACAAGGGCTTAAT
*
41458321 TGCTTTATTTGAAAAAGTTTGAGGG
65 TGCTTTTTTTGAAAAAGTTTGAGGG
* * * * *
41458346 CCTTTTAATGTATTTTTTAAAGTTCAAGTACCCAATTGAGTGAAAAAAAAAAGCAGGGGCCTAAT
1 CTTTTTAATGCA-TTTTTAAAGTTCAAGTACCCAATTGAGTGAAAAAAAAAAACAAGGGCTTAAT
****
41458411 T--TTTTTTTTTTTAAGTTTGAGGG
65 TGCTTTTTTTGAAAAAGTTTGAGGG
* * *
41458434 CATTTTTTATGCATTTTGAAAGTTCAAATACCCAATTGAGTGAAAAAAAAAAACAAGGGCTTAAT
1 C-TTTTTAATGCATTTTTAAAGTTCAAGTACCCAATTGAGTGAAAAAAAAAAACAAGGGCTTAAT
*
41458499 TGCTTTTTTTGAAAAAGCTTGAGGG
65 TGCTTTTTTTGAAAAAGTTTGAGGG
41458524 CTTTTT
1 CTTTTT
41458530 TACACCCTTA
Statistics
Matches: 152, Mismatches: 26, Indels: 11
0.80 0.14 0.06
Matches are distributed among these distances:
88 76 0.50
89 15 0.10
90 61 0.40
ACGTcount: A:0.34, C:0.11, G:0.17, T:0.38
Consensus pattern (89 bp):
CTTTTTAATGCATTTTTAAAGTTCAAGTACCCAATTGAGTGAAAAAAAAAAACAAGGGCTTAATT
GCTTTTTTTGAAAAAGTTTGAGGG
Found at i:41459992 original size:16 final size:15
Alignment explanation
Indices: 41459971--41460021 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
41459961 TTTTAGCAAC
41459971 TTTTTACTTACAAATA
1 TTTTTA-TTACAAATA
*
41459987 TTTTTATTGCATAA-A
1 TTTTTATTACA-AATA
* *
41460002 TTTTTATGACCAATA
1 TTTTTATTACAAATA
41460017 TTTTT
1 TTTTT
41460022 TAAAAGGTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
14 2 0.07
15 19 0.66
16 8 0.28
ACGTcount: A:0.31, C:0.10, G:0.04, T:0.55
Consensus pattern (15 bp):
TTTTTATTACAAATA
Found at i:41464601 original size:58 final size:58
Alignment explanation
Indices: 41464506--41464618 Score: 172
Period size: 58 Copynumber: 1.9 Consensus size: 58
41464496 CTTGGCTTCA
** * * *
41464506 ATAGATACCTTGTTCCTTTCTGAAAGGTTAGCCTTGACAAGTGAAATGGTAAGGCTGG
1 ATAGATACCTTGTTCCTTTCCAAAAGGCTAGCATTGACAAATGAAATGGTAAGGCTGG
*
41464564 ATAGATCCCTTGTTCCTTTCCAAAAGGCTAGCATTGACAAATGAAATGGTAAGGC
1 ATAGATACCTTGTTCCTTTCCAAAAGGCTAGCATTGACAAATGAAATGGTAAGGC
41464619 AGAAATTGTT
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
58 49 1.00
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (58 bp):
ATAGATACCTTGTTCCTTTCCAAAAGGCTAGCATTGACAAATGAAATGGTAAGGCTGG
Found at i:41472629 original size:16 final size:18
Alignment explanation
Indices: 41472608--41472644 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
41472598 TCAATATCAG
41472608 TCAAT-ATTTT-TCAATA
1 TCAATAATTTTATCAATA
41472624 TCAATAATTTTATCAATA
1 TCAATAATTTTATCAATA
41472642 TCA
1 TCA
41472645 TTCAGTAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 5 0.26
17 5 0.26
18 9 0.47
ACGTcount: A:0.41, C:0.14, G:0.00, T:0.46
Consensus pattern (18 bp):
TCAATAATTTTATCAATA
Found at i:41472667 original size:18 final size:18
Alignment explanation
Indices: 41472644--41472722 Score: 113
Period size: 18 Copynumber: 4.4 Consensus size: 18
41472634 TATCAATATC
41472644 ATTCAGTAACAATCAATT
1 ATTCAGTAACAATCAATT
* *
41472662 ATTCAGTAGCAATCAGTT
1 ATTCAGTAACAATCAATT
41472680 ATTCAGTAACAATCAATT
1 ATTCAGTAACAATCAATT
* * *
41472698 ATTCAGTAACAGTCAGTC
1 ATTCAGTAACAATCAATT
41472716 ATTCAGT
1 ATTCAGT
41472723 GCCTTTATTC
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 54 1.00
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.33
Consensus pattern (18 bp):
ATTCAGTAACAATCAATT
Found at i:41472685 original size:36 final size:36
Alignment explanation
Indices: 41472642--41472722 Score: 135
Period size: 36 Copynumber: 2.2 Consensus size: 36
41472632 TTTATCAATA
*
41472642 TCATTCAGTAACAATCAATTATTCAGTAGCAATCAG
1 TCATTCAGTAACAATCAATTATTCAGTAACAATCAG
* *
41472678 TTATTCAGTAACAATCAATTATTCAGTAACAGTCAG
1 TCATTCAGTAACAATCAATTATTCAGTAACAATCAG
41472714 TCATTCAGT
1 TCATTCAGT
41472723 GCCTTTATTC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (36 bp):
TCATTCAGTAACAATCAATTATTCAGTAACAATCAG
Found at i:41472966 original size:44 final size:44
Alignment explanation
Indices: 41472876--41472967 Score: 123
Period size: 44 Copynumber: 2.1 Consensus size: 44
41472866 CCGAAGTAAC
* * *
41472876 AGTAACAGTACGACACACATGGTGCCTCATCGACTCGAAGTTGA
1 AGTAACAATACGACACACATAGTGCCTCATCGACTCGAAGTCGA
**
41472920 AGTAACAATACGACACTTATAGTGCCTCATCGACTC-AAGGTCGA
1 AGTAACAATACGACACACATAGTGCCTCATCGACTCGAA-GTCGA
41472964 AGTA
1 AGTA
41472968 TCCCTGAACA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
43 2 0.05
44 40 0.95
ACGTcount: A:0.34, C:0.24, G:0.21, T:0.22
Consensus pattern (44 bp):
AGTAACAATACGACACACATAGTGCCTCATCGACTCGAAGTCGA
Found at i:41473476 original size:20 final size:20
Alignment explanation
Indices: 41473439--41473476 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
41473429 TTACCATACA
*
41473439 AATTAAATAATAATTTCAAC
1 AATTAAATAATAAGTTCAAC
*
41473459 AATTAAATATTAAGTTCA
1 AATTAAATAATAAGTTCA
41473477 GATTATAGAA
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:0.53, C:0.08, G:0.03, T:0.37
Consensus pattern (20 bp):
AATTAAATAATAAGTTCAAC
Found at i:41473625 original size:13 final size:12
Alignment explanation
Indices: 41473599--41473639 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 12
41473589 AATCCCTAGT
*
41473599 TTTTCCTTTTTC
1 TTTTCTTTTTTC
41473611 TTTTCTTTTTCTC
1 TTTTCTTTTT-TC
41473624 TTTTCTTTCTTTC
1 TTTTCTTT-TTTC
41473637 TTT
1 TTT
41473640 CCCGTTTGCT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
12 9 0.35
13 15 0.58
14 2 0.08
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (12 bp):
TTTTCTTTTTTC
Found at i:41473743 original size:12 final size:13
Alignment explanation
Indices: 41473717--41473752 Score: 58
Period size: 12 Copynumber: 2.9 Consensus size: 13
41473707 ATATTAGTTA
41473717 ATAATAATATATT
1 ATAATAATATATT
41473730 ATAATAAT-TATT
1 ATAATAATATATT
41473742 ATAATAA-ATAT
1 ATAATAATATAT
41473753 CTATTTAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 14 0.64
13 8 0.36
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
ATAATAATATATT
Found at i:41477766 original size:19 final size:19
Alignment explanation
Indices: 41477734--41477788 Score: 74
Period size: 19 Copynumber: 2.9 Consensus size: 19
41477724 ATGCGTCAAG
* * *
41477734 ATGCACTTTGTGTGCTAGT
1 ATGCACTATATGTGCCAGT
*
41477753 ATGCATTATATGTGCCAGT
1 ATGCACTATATGTGCCAGT
41477772 ATGCACTATATGTGCCA
1 ATGCACTATATGTGCCA
41477789 ATTTTCCCTT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.36
Consensus pattern (19 bp):
ATGCACTATATGTGCCAGT
Found at i:41484198 original size:174 final size:174
Alignment explanation
Indices: 41483894--41484215 Score: 520
Period size: 174 Copynumber: 1.9 Consensus size: 174
41483884 AGCCCTCTAA
* * * *
41483894 CTCTAACTTATTTTCTAATTCTACTAAAATTCCTTATTTATTATTTTATCAAATTGAAACCCTAG
1 CTCTAACTCATTTCCTAATTCTACTAAAATTCCCTATTTATTATTTTATCAAATTGAAACCCTAA
*
41483959 CTTTCTCTATTTAAACCCTAGTTTTCTATCAAAATTCTCTATTTCAAAAATCTTTTAATCCCTTA
66 CTCTCTCTATTTAAACCCTAGTTTTCTATCAAAATTCTCTATTTCAAAAATCTTTTAATCCCTTA
41484024 AGTTCTACTGAAAAATAACTCATTTGGCCATTAGTCCTTAAATT
131 AGTTCTACTGAAAAATAACTCATTTGGCCATTAGTCCTTAAATT
* *
41484068 CTCTAAGTCATTTCCTAATTCTACTAAAATTCCCTATTTGTTATTTTATCAAATTGAAACCCTAA
1 CTCTAACTCATTTCCTAATTCTACTAAAATTCCCTATTTATTATTTTATCAAATTGAAACCCTAA
* * *
41484133 CTCTCTCTATTTATAACCC-AGTTTTCTCTTAAAATTCTCTATTTCAAAACTCTTTTAATCCCTT
66 CTCTCTCTATTTA-AACCCTAGTTTTCTATCAAAATTCTCTATTTCAAAAATCTTTTAATCCCTT
* *
41484197 AAGTTTTGCTGAAAAATAA
130 AAGTTCTACTGAAAAATAA
41484216 TCTTTAAAGT
Statistics
Matches: 135, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
174 130 0.96
175 5 0.04
ACGTcount: A:0.31, C:0.21, G:0.05, T:0.43
Consensus pattern (174 bp):
CTCTAACTCATTTCCTAATTCTACTAAAATTCCCTATTTATTATTTTATCAAATTGAAACCCTAA
CTCTCTCTATTTAAACCCTAGTTTTCTATCAAAATTCTCTATTTCAAAAATCTTTTAATCCCTTA
AGTTCTACTGAAAAATAACTCATTTGGCCATTAGTCCTTAAATT
Found at i:41486341 original size:16 final size:16
Alignment explanation
Indices: 41486322--41486372 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
41486312 AGATATATTG
*
41486322 ATATATAGATTTACAT
1 ATATATAGATATACAT
* * *
41486338 ATATACAAATATACAA
1 ATATATAGATATACAT
41486354 ATATATAGATATA-AT
1 ATATATAGATATACAT
41486369 ATAT
1 ATAT
41486373 GCTTATACAA
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
15 5 0.18
16 23 0.82
ACGTcount: A:0.53, C:0.06, G:0.04, T:0.37
Consensus pattern (16 bp):
ATATATAGATATACAT
Found at i:41489949 original size:18 final size:19
Alignment explanation
Indices: 41489906--41489947 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 19
41489896 AATGGCTTCC
41489906 AAAAAA-TTATTTTT-TAA
1 AAAAAATTTATTTTTCTAA
41489923 AAAATAATTTATTTTTCTAGA
1 AAAA-AATTTATTTTTCTA-A
41489944 AAAA
1 AAAA
41489948 TTAATATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
17 4 0.19
18 2 0.10
19 8 0.38
20 2 0.10
21 5 0.24
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (19 bp):
AAAAAATTTATTTTTCTAA
Found at i:41490016 original size:31 final size:32
Alignment explanation
Indices: 41489950--41490021 Score: 85
Period size: 31 Copynumber: 2.2 Consensus size: 32
41489940 TAGAAAAATT
* *
41489950 AATATTTTCTGGTGTTTAGATAAATTTGTGTAA
1 AATA-TTTCTGGTGTTTAGACAAATTTCTGTAA
*
41489983 AATATTTCTGTTGTTT-GACAAATTTCT-TAAA
1 AATATTTCTGGTGTTTAGACAAATTTCTGT-AA
41490014 AATATTTC
1 AATATTTC
41490022 ATAAAAGTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
30 1 0.03
31 19 0.54
32 11 0.31
33 4 0.11
ACGTcount: A:0.32, C:0.07, G:0.12, T:0.49
Consensus pattern (32 bp):
AATATTTCTGGTGTTTAGACAAATTTCTGTAA
Found at i:41490513 original size:13 final size:14
Alignment explanation
Indices: 41490475--41490516 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
41490465 TATGTGAATA
41490475 ATATTATTTAAAATT
1 ATATTA-TTAAAATT
*
41490490 ATAATTTTTAAAATT
1 AT-ATTATTAAAATT
41490505 -TATTATTAAAAT
1 ATATTATTAAAAT
41490517 AAAATTGAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 10 0.42
14 1 0.04
15 10 0.42
16 3 0.12
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
ATATTATTAAAATT
Found at i:41490551 original size:16 final size:19
Alignment explanation
Indices: 41490532--41490581 Score: 52
Period size: 18 Copynumber: 2.6 Consensus size: 19
41490522 TGAACTATTA
41490532 AATAATTTATTAA-A-AT-
1 AATAATTTATTAATATATC
41490548 AATAAATTATATTAATTATATC
1 AAT-AATT-TATTAA-TATATC
41490570 AATAATTTATTA
1 AATAATTTATTA
41490582 TATGAATAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
16 3 0.11
17 4 0.14
18 6 0.21
20 6 0.21
21 6 0.21
22 3 0.11
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (19 bp):
AATAATTTATTAATATATC
Found at i:41491580 original size:16 final size:18
Alignment explanation
Indices: 41491553--41491587 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
41491543 TCCTCTTCAT
41491553 CCTCTATTTC-TTTTCTC
1 CCTCTATTTCTTTTTCTC
41491570 CCTCT-TTTCTTTTTCTC
1 CCTCTATTTCTTTTTCTC
41491587 C
1 C
41491588 TATTTTCTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.03, C:0.37, G:0.00, T:0.60
Consensus pattern (18 bp):
CCTCTATTTCTTTTTCTC
Found at i:41491593 original size:16 final size:17
Alignment explanation
Indices: 41491559--41491595 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
41491549 TCATCCTCTA
*
41491559 TTTC-TTTTCTCCCTCT
1 TTTCTTTTTCTCCCTAT
41491575 TTTCTTTTTCT-CCTAT
1 TTTCTTTTTCTCCCTAT
41491591 TTTCT
1 TTTCT
41491596 CTCATAAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.03, C:0.30, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTCTTTTTCTCCCTAT
Found at i:41492631 original size:43 final size:43
Alignment explanation
Indices: 41492580--41492826 Score: 247
Period size: 43 Copynumber: 5.8 Consensus size: 43
41492570 GAAAAGTGAC
* *
41492580 ATTTTATCTGCAAATATGTTGTGCATCCACAGCCCAGTGGCAG
1 ATTTTATCTACAAATATGTTGTGCATCCACAACCCAGTGGCAG
* * * *
41492623 ATTTTATCTACAACA-ATGTTGTGCACCCACAGCCCACTGACAG
1 ATTTTATCTACAA-ATATGTTGTGCATCCACAACCCAGTGGCAG
* * * * ** *
41492666 TTTTTATCTTCAAATATGTTGTGTATCCACAACTCAACGACA-
1 ATTTTATCTACAAATATGTTGTGCATCCACAACCCAGTGGCAG
*
41492708 ATTTTTATCTGCAAATATGTTGTGCATCCACAACCCAGTGGCA-
1 A-TTTTATCTACAAATATGTTGTGCATCCACAACCCAGTGGCAG
***
41492751 A-TTTATCTACAAATATAACGTGCATCCACAACCCAGTGGTC-G
1 ATTTTATCTACAAATATGTTGTGCATCCACAACCCAGTGG-CAG
* *
41492793 --TTTATCTATAAATATGTTGTGCATCCACAGCCCA
1 ATTTTATCTACAAATATGTTGTGCATCCACAACCCA
41492827 ATGGTGGTTT
Statistics
Matches: 171, Mismatches: 28, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
41 63 0.37
42 2 0.01
43 105 0.61
44 1 0.01
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.31
Consensus pattern (43 bp):
ATTTTATCTACAAATATGTTGTGCATCCACAACCCAGTGGCAG
Found at i:41495815 original size:65 final size:65
Alignment explanation
Indices: 41495706--41495837 Score: 246
Period size: 65 Copynumber: 2.0 Consensus size: 65
41495696 TTCCCATATG
*
41495706 TATTCTCGATGAGCTACCAGGGTTACCTCCAAACCGTGAAGTTTAATTCAAAATTGAGTTGTTGC
1 TATTCTCGATGAGCTACCAGGGTTACCTCCAAACCATGAAGTTTAATTCAAAATTGAGTTGTTGC
*
41495771 TATTCTCGATGAGCTACCAGGGTTACCTCCAAACCATGAGGTTTAATTCAAAATTGAGTTGTTGC
1 TATTCTCGATGAGCTACCAGGGTTACCTCCAAACCATGAAGTTTAATTCAAAATTGAGTTGTTGC
41495836 TA
1 TA
41495838 GAAACTACTC
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
65 65 1.00
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.33
Consensus pattern (65 bp):
TATTCTCGATGAGCTACCAGGGTTACCTCCAAACCATGAAGTTTAATTCAAAATTGAGTTGTTGC
Found at i:41500862 original size:17 final size:17
Alignment explanation
Indices: 41500840--41500887 Score: 51
Period size: 18 Copynumber: 2.8 Consensus size: 17
41500830 ACTAAAATTC
41500840 CTTTTCATCCTCTATTT
1 CTTTTCATCCTCTATTT
* * *
41500857 CTTTTCTTCCTTTTTTTT
1 CTTTTCATCC-TCTATTT
*
41500875 CTTTTCCTCCTCT
1 CTTTTCATCCTCT
41500888 TTTATCACAT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
17 11 0.44
18 14 0.56
ACGTcount: A:0.04, C:0.31, G:0.00, T:0.65
Consensus pattern (17 bp):
CTTTTCATCCTCTATTT
Found at i:41500877 original size:18 final size:19
Alignment explanation
Indices: 41500854--41500890 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
41500844 TCATCCTCTA
*
41500854 TTTCTTTTCTTCCT-TTTT
1 TTTCTTTTCCTCCTCTTTT
41500872 TTTCTTTTCCTCCTCTTTT
1 TTTCTTTTCCTCCTCTTTT
41500891 ATCACATCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (19 bp):
TTTCTTTTCCTCCTCTTTT
Found at i:41503686 original size:18 final size:18
Alignment explanation
Indices: 41503663--41503700 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
41503653 TTCATACAAA
41503663 TTCCAGTTTAAACTAAAT
1 TTCCAGTTTAAACTAAAT
41503681 TTCCAGTTTAAACTAAAT
1 TTCCAGTTTAAACTAAAT
41503699 TT
1 TT
41503701 AACTCCCTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.37, C:0.16, G:0.05, T:0.42
Consensus pattern (18 bp):
TTCCAGTTTAAACTAAAT
Found at i:41511070 original size:25 final size:23
Alignment explanation
Indices: 41511042--41511087 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
41511032 ACTTTAATTA
41511042 ATATAATATATAAAATAAATTTAAC
1 ATATAATATAT-AAAT-AATTTAAC
*
41511067 ATATAATTTATAAATAATTTA
1 ATATAATATATAAATAATTTA
41511088 CTAATGCCGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 4 0.20
25 10 0.50
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (23 bp):
ATATAATATATAAATAATTTAAC
Found at i:41513046 original size:16 final size:16
Alignment explanation
Indices: 41513027--41513068 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
41513017 TAATTGATCG
41513027 AATTAATAATAAATTT
1 AATTAATAATAAATTT
*
41513043 AATTTAATTA-AAATTT
1 AA-TTAATAATAAATTT
41513059 AATTAATAAT
1 AATTAATAAT
41513069 TTTGATTATC
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 6 0.27
16 10 0.45
17 6 0.27
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AATTAATAATAAATTT
Found at i:41513057 original size:11 final size:12
Alignment explanation
Indices: 41513042--41513070 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
41513032 ATAATAAATT
41513042 TAATTTAATTAA
1 TAATTTAATTAA
41513054 -AATTTAATTAA
1 TAATTTAATTAA
41513065 TAATTT
1 TAATTT
41513071 TGATTATCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TAATTTAATTAA
Found at i:41514142 original size:33 final size:31
Alignment explanation
Indices: 41514103--41514211 Score: 100
Period size: 33 Copynumber: 3.4 Consensus size: 31
41514093 AGAAAGTGGT
41514103 AAGAGAACAAGTTGATTGAGAGATATAGAAAG
1 AAGAGAACAAGTTGA-TGAGAGATATAGAAAG
* *
41514135 AGAGAGAACAAGTTTAGATGCG-GA-A-AG-GAG
1 A-AGAGAACAAG-TT-GATGAGAGATATAGAAAG
41514165 CAAGAGAACAAGTTGACTGAGAGATATAGAAAG
1 -AAGAGAACAAGTTGA-TGAGAGATATAGAAAG
*
41514198 AACGAGCACAAGTT
1 AA-GAGAACAAGTT
41514212 TGCTTAGAAT
Statistics
Matches: 62, Mismatches: 5, Indels: 19
0.72 0.06 0.22
Matches are distributed among these distances:
28 2 0.03
29 5 0.08
30 14 0.23
31 4 0.06
32 6 0.10
33 24 0.39
34 5 0.08
35 2 0.03
ACGTcount: A:0.47, C:0.08, G:0.29, T:0.16
Consensus pattern (31 bp):
AAGAGAACAAGTTGATGAGAGATATAGAAAG
Found at i:41516379 original size:21 final size:22
Alignment explanation
Indices: 41516346--41516386 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
41516336 TAAACATATT
41516346 TTAATTTTATAAA-AAAAATTA
1 TTAATTTTATAAATAAAAATTA
41516367 TTAATATTT-TAAATAAAAAT
1 TTAAT-TTTATAAATAAAAAT
41516387 AATAATACGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
TTAATTTTATAAATAAAAATTA
Found at i:41516392 original size:21 final size:23
Alignment explanation
Indices: 41516349--41516393 Score: 58
Period size: 21 Copynumber: 2.0 Consensus size: 23
41516339 ACATATTTTA
*
41516349 ATTTTATAAAAAAAATTATTAAT
1 ATTTTATAAAAAAAATTAATAAT
*
41516372 ATTTTA-AATAAAAA-TAATAAT
1 ATTTTATAAAAAAAATTAATAAT
41516393 A
1 A
41516394 CGAAACATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 7 0.35
22 7 0.35
23 6 0.30
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (23 bp):
ATTTTATAAAAAAAATTAATAAT
Found at i:41517872 original size:28 final size:28
Alignment explanation
Indices: 41517841--41517952 Score: 70
Period size: 28 Copynumber: 3.9 Consensus size: 28
41517831 TAATATAATT
41517841 ATATTTATAAAAATATTTAAATAATTTA
1 ATATTTATAAAAATATTTAAATAATTTA
* * *
41517869 ATATAATGATAGATAAA-ATATGAATTAATTTA
1 ATAT--TTATA-A-AAATAT-TTAAATAATTTA
*
41517901 A-ATTTTTAAATACAT-TTTAAATAA-TTA
1 ATATTTATAAA-A-ATATTTAAATAATTTA
** *
41517928 ATATAAATAAAAATATTTTAATAAT
1 ATATTTATAAAAATATTTAAATAAT
41517953 CTATACTTTA
Statistics
Matches: 62, Mismatches: 11, Indels: 22
0.65 0.12 0.23
Matches are distributed among these distances:
26 2 0.03
27 14 0.23
28 18 0.29
29 5 0.08
30 4 0.06
31 5 0.08
32 14 0.23
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.43
Consensus pattern (28 bp):
ATATTTATAAAAATATTTAAATAATTTA
Found at i:41521986 original size:36 final size:36
Alignment explanation
Indices: 41521932--41522003 Score: 92
Period size: 36 Copynumber: 2.0 Consensus size: 36
41521922 GTGCAGGAGT
*
41521932 TTGAGAAGACTCGATATCTCATTCAAGATCTTGGGA
1 TTGAGAAGACTCGATATCTCATTCAAGAGCTTGGGA
* * *
41521968 TTGAGAAGAC-CTGGTATCTCGTTGAAGAGCTTGGGA
1 TTGAGAAGACTC-GATATCTCATTCAAGAGCTTGGGA
41522004 ATATATGATA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
35 1 0.03
36 30 0.97
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.29
Consensus pattern (36 bp):
TTGAGAAGACTCGATATCTCATTCAAGAGCTTGGGA
Found at i:41523617 original size:3 final size:3
Alignment explanation
Indices: 41523609--41523639 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
41523599 AAGTTTTCTT
*
41523609 TTA TTA TTA TTA TTT TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
41523640 CATCTGTGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:41523627 original size:15 final size:15
Alignment explanation
Indices: 41523607--41523637 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
41523597 AGAAGTTTTC
41523607 TTTTATTATTATTAT
1 TTTTATTATTATTAT
41523622 TTTTATTATTATTAT
1 TTTTATTATTATTAT
41523637 T
1 T
41523638 ATCATCTGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTTATTATTATTAT
Found at i:41532311 original size:21 final size:20
Alignment explanation
Indices: 41532277--41532315 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
41532267 AAAAATAAAC
41532277 AACTTCACATTTTTTAAAGT
1 AACTTCACATTTTTTAAAGT
*
41532297 AACTTTACAATTTTTTAAA
1 AACTTCAC-ATTTTTTAAA
41532316 ATTTATATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.38, C:0.13, G:0.03, T:0.46
Consensus pattern (20 bp):
AACTTCACATTTTTTAAAGT
Found at i:41533616 original size:44 final size:44
Alignment explanation
Indices: 41533553--41533641 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
41533543 ATTATTTCAA
41533553 AGATAAAGTTATTTTAGAGTAATATCCATGTGATTTTTGAATTT
1 AGATAAAGTTATTTTAGAGTAATATCCATGTGATTTTTGAATTT
41533597 AGATAAAGTTATTTTAGAGTAATATCCATGTGATTTTTGAATTT
1 AGATAAAGTTATTTTAGAGTAATATCCATGTGATTTTTGAATTT
41533641 A
1 A
41533642 AATTGATATG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.35, C:0.04, G:0.16, T:0.45
Consensus pattern (44 bp):
AGATAAAGTTATTTTAGAGTAATATCCATGTGATTTTTGAATTT
Found at i:41533632 original size:22 final size:22
Alignment explanation
Indices: 41533563--41533633 Score: 63
Period size: 22 Copynumber: 3.2 Consensus size: 22
41533553 AGATAAAGTT
41533563 ATTTTAGAGTAATATCCATGTG
1 ATTTTAGAGTAATATCCATGTG
* * * * * * *
41533585 ATTTTTGAATTTAGAT-AAAGTT
1 ATTTTAG-AGTAATATCCATGTG
41533607 ATTTTAGAGTAATATCCATGTG
1 ATTTTAGAGTAATATCCATGTG
41533629 ATTTT
1 ATTTT
41533634 TGAATTTAAA
Statistics
Matches: 33, Mismatches: 14, Indels: 4
0.65 0.27 0.08
Matches are distributed among these distances:
21 5 0.15
22 23 0.70
23 5 0.15
ACGTcount: A:0.32, C:0.06, G:0.15, T:0.46
Consensus pattern (22 bp):
ATTTTAGAGTAATATCCATGTG
Found at i:41536565 original size:5 final size:5
Alignment explanation
Indices: 41536555--41536582 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
41536545 AATAATTAAG
41536555 TATAT TATAT TATAT TATAT TATAT TAT
1 TATAT TATAT TATAT TATAT TATAT TAT
41536583 TATATATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TATAT
Found at i:41536657 original size:31 final size:30
Alignment explanation
Indices: 41536622--41536682 Score: 70
Period size: 30 Copynumber: 2.0 Consensus size: 30
41536612 GAAACAGAAT
*
41536622 GAAAGCAAACGAAAC-AGAGAAGAACAGGGGA
1 GAAAG-AAACGAAACAAGA-AAGAAAAGGGGA
* *
41536653 GAAAGAAAGGAAAGAAGAAAGAAAAGGGGA
1 GAAAGAAACGAAACAAGAAAGAAAAGGGGA
41536683 AATAAGGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
30 18 0.69
31 8 0.31
ACGTcount: A:0.59, C:0.07, G:0.34, T:0.00
Consensus pattern (30 bp):
GAAAGAAACGAAACAAGAAAGAAAAGGGGA
Found at i:41538260 original size:39 final size:39
Alignment explanation
Indices: 41538153--41538287 Score: 123
Period size: 39 Copynumber: 3.4 Consensus size: 39
41538143 GACCTCGAGT
* * *
41538153 CGATGAGACACTGGGTGTC-ACTATATTTCTTCGGATAGATT
1 CGATGAGACACTGGGTGTCAAC--TATTACTTCGGCTAG-TC
** ** *
41538194 CGATGAGGTACTGGGTACCAACT-TTACTTCGGCTAGGC
1 CGATGAGACACTGGGTGTCAACTATTACTTCGGCTAGTC
*
41538232 CGATGAGACACTGGGTGTCAACTATTACTTCGAACTA-TC
1 CGATGAGACACTGGGTGTCAACTATTACTTCG-GCTAGTC
*
41538271 CGATGAGGCACTGGGTG
1 CGATGAGACACTGGGTG
41538288 CCATATTGGT
Statistics
Matches: 76, Mismatches: 15, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
38 19 0.25
39 36 0.47
40 4 0.05
41 15 0.20
42 2 0.03
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (39 bp):
CGATGAGACACTGGGTGTCAACTATTACTTCGGCTAGTC
Found at i:41545926 original size:4 final size:4
Alignment explanation
Indices: 41545917--41545948 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
41545907 CCCTTTCCTT
*
41545917 TTTC TTTC TTTC TTTT TTTC TTTC TTTC TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
41545949 CTCTGTTTCG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTC
Found at i:41545936 original size:16 final size:16
Alignment explanation
Indices: 41545915--41545947 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
41545905 TTCCCTTTCC
41545915 TTTTTCTTTCTTTCTT
1 TTTTTCTTTCTTTCTT
41545931 TTTTTCTTTCTTTCTT
1 TTTTTCTTTCTTTCTT
41545947 T
1 T
41545948 CCTCTGTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (16 bp):
TTTTTCTTTCTTTCTT
Found at i:41552454 original size:56 final size:56
Alignment explanation
Indices: 41552389--41552499 Score: 170
Period size: 56 Copynumber: 2.0 Consensus size: 56
41552379 TTCGTAAGCT
41552389 TCGATGCTCACACAGAGCTACAATAGTCCACAA-TATATGCGGAATACTACCAATCC
1 TCGATGCTCACACAGAGCTACAATAGTCCACAACT-TATGCGGAATACTACCAATCC
** **
41552445 TCGATGCTCACACAGAGCTACGGTAGTCTGCAACTTATGCGGAATACTACCAATC
1 TCGATGCTCACACAGAGCTACAATAGTCCACAACTTATGCGGAATACTACCAATC
41552500 ACTATACTCA
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
56 49 0.98
57 1 0.02
ACGTcount: A:0.32, C:0.28, G:0.17, T:0.23
Consensus pattern (56 bp):
TCGATGCTCACACAGAGCTACAATAGTCCACAACTTATGCGGAATACTACCAATCC
Found at i:41553409 original size:5 final size:5
Alignment explanation
Indices: 41553392--41553438 Score: 53
Period size: 5 Copynumber: 9.6 Consensus size: 5
41553382 TTTAATGATA
* *
41553392 ATAAT ATATT ATAAT ATAGT AATAAT AT-A- ATAAT ATAAT ATAAT ATA
1 ATAAT ATAAT ATAAT ATAAT -ATAAT ATAAT ATAAT ATAAT ATAAT ATA
41553439 TTAGTTATGC
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
3 2 0.06
4 2 0.06
5 27 0.77
6 4 0.11
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (5 bp):
ATAAT
Done.