Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008323.1 Hibiscus syriacus cultivar Beakdansim tig00111027_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 5101972
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 26
Found at i:1193496 original size:11 final size:10
Alignment explanation
Indices: 1193451--1193507 Score: 53
Period size: 10 Copynumber: 5.5 Consensus size: 10
1193441 TTGCATTCTT
1193451 TTTTTATTGA
1 TTTTTATTGA
* *
1193461 ATTTTATTCA
1 TTTTTATTGA
*
1193471 CTTTTAATT-A
1 -TTTTTATTGA
1193481 TTTTTTATTGTA
1 -TTTTTATTG-A
1193493 TTTTTATTGA
1 TTTTTATTGA
1193503 TTTTT
1 TTTTT
1193508 TAAAAAAATG
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
10 22 0.58
11 15 0.39
12 1 0.03
ACGTcount: A:0.21, C:0.04, G:0.05, T:0.70
Consensus pattern (10 bp):
TTTTTATTGA
Found at i:1193508 original size:11 final size:11
Alignment explanation
Indices: 1193450--1193509 Score: 54
Period size: 11 Copynumber: 5.6 Consensus size: 11
1193440 TTTGCATTCT
1193450 TTTTTTATTGA
1 TTTTTTATTGA
* *
1193461 -ATTTTATTCA
1 TTTTTTATTGA
* *
1193471 CTTTTAATT-A
1 TTTTTTATTGA
1193481 TTTTTTATTG-
1 TTTTTTATTGA
1193491 TATTTTTATTGA
1 T-TTTTTATTGA
1193503 TTTTTTA
1 TTTTTTA
1193510 AAAAAATGAA
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
10 17 0.44
11 21 0.54
12 1 0.03
ACGTcount: A:0.22, C:0.03, G:0.05, T:0.70
Consensus pattern (11 bp):
TTTTTTATTGA
Found at i:1196965 original size:60 final size:60
Alignment explanation
Indices: 1196869--1197024 Score: 144
Period size: 60 Copynumber: 2.6 Consensus size: 60
1196859 CTTATTATTC
* *
1196869 TAAACTTTAGAATA-TTCTAATTTCATCCTCAAACTAT-AACTATTATTTTAAA-TTAGTCTA
1 TAAACTTTTGAATATTTC-AATTTCATCCTCAAACTATGAACT-TTATTCTAAATTTAGTC-A
* * * * *
1196929 TAAACTTTTGAATATTTCAATTTTATTCCT-AGACTATGATCTTTATTCTAAATTTATTCC
1 TAAACTTTTGAATATTTCAATTTCA-TCCTCAAACTATGAACTTTATTCTAAATTTAGTCA
* *
1196989 TAAACTTTTAAACATTTCAA-TTCTATCC-CAAACTAT
1 TAAACTTTTGAATATTTCAATTTC-ATCCTCAAACTAT
1197025 ATGTATATTC
Statistics
Matches: 79, Mismatches: 11, Indels: 13
0.77 0.11 0.13
Matches are distributed among these distances:
59 11 0.14
60 53 0.67
61 15 0.19
ACGTcount: A:0.35, C:0.17, G:0.03, T:0.45
Consensus pattern (60 bp):
TAAACTTTTGAATATTTCAATTTCATCCTCAAACTATGAACTTTATTCTAAATTTAGTCA
Found at i:1197217 original size:60 final size:60
Alignment explanation
Indices: 1197144--1197261 Score: 157
Period size: 60 Copynumber: 2.0 Consensus size: 60
1197134 ATATTTGAAT
* * *
1197144 TAATTTTGGGATGAAATTGGAA-GATTCAAAAGTTTAAAGATTAATTTAGAATGAGAGTCA
1 TAATTTTGCGATGAAATTGAAATG-TTCAAAAGTTTAAAGACTAATTTAGAATGAGAGTCA
* * * *
1197204 TAATTTTGCGATGAGATTGAAATGTTCAAAAGTTTAAGGACTAGTTTAGATTGAGAGT
1 TAATTTTGCGATGAAATTGAAATGTTCAAAAGTTTAAAGACTAATTTAGAATGAGAGT
1197262 TATAGTTCGG
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
60 49 0.98
61 1 0.02
ACGTcount: A:0.38, C:0.04, G:0.23, T:0.35
Consensus pattern (60 bp):
TAATTTTGCGATGAAATTGAAATGTTCAAAAGTTTAAAGACTAATTTAGAATGAGAGTCA
Found at i:1197277 original size:60 final size:59
Alignment explanation
Indices: 1197168--1197281 Score: 138
Period size: 60 Copynumber: 1.9 Consensus size: 59
1197158 AATTGGAAGA
* **
1197168 TTCAAAAGTTTAAAGATTAATTTAGAATGAGAGTCATAATTTTGCGATGAGATTGAAATG
1 TTCAAAAGTTTAAAGACTAATTTAGAATGAGAGTCATAATTCGGCGATGA-ATTGAAATG
* * * * * *
1197228 TTCAAAAGTTTAAGGACTAGTTTAGATTGAGAGTTATAGTTCGGTGATGAATTG
1 TTCAAAAGTTTAAAGACTAATTTAGAATGAGAGTCATAATTCGGCGATGAATTG
1197282 GAATATCCAA
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
59 4 0.09
60 41 0.91
ACGTcount: A:0.36, C:0.05, G:0.23, T:0.36
Consensus pattern (59 bp):
TTCAAAAGTTTAAAGACTAATTTAGAATGAGAGTCATAATTCGGCGATGAATTGAAATG
Found at i:1199278 original size:15 final size:15
Alignment explanation
Indices: 1199258--1199290 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1199248 TGAGACATTA
*
1199258 CCCGCCCCGCATCCG
1 CCCGCCCCACATCCG
1199273 CCCGCCCCACATCCG
1 CCCGCCCCACATCCG
1199288 CCC
1 CCC
1199291 ACCAGCTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.09, C:0.70, G:0.15, T:0.06
Consensus pattern (15 bp):
CCCGCCCCACATCCG
Found at i:1200258 original size:54 final size:54
Alignment explanation
Indices: 1200143--1200258 Score: 119
Period size: 54 Copynumber: 2.2 Consensus size: 54
1200133 TAAAGTGCAC
* * * **
1200143 AATATT-AATATTTTCGGTAGAAAAAATAATGTTTTAGATAGTATTTTATCGGA
1 AATATTAAACATTTTCGGTAGAAAAAATAATATTTTAGATAGTATTTTACCAAA
* * * * *
1200196 TATGTTAAACATTTTCGGTATAAATAATAATATTTTAGGTAAGT-TTTTACCAAA
1 AATATTAAACATTTTCGGTAGAAAAAATAATATTTTAGAT-AGTATTTTACCAAA
1200250 AATATTAAA
1 AATATTAAA
1200259 AAAATAATAA
Statistics
Matches: 49, Mismatches: 12, Indels: 3
0.77 0.19 0.05
Matches are distributed among these distances:
53 4 0.08
54 42 0.86
55 3 0.06
ACGTcount: A:0.41, C:0.05, G:0.12, T:0.41
Consensus pattern (54 bp):
AATATTAAACATTTTCGGTAGAAAAAATAATATTTTAGATAGTATTTTACCAAA
Found at i:1208937 original size:21 final size:23
Alignment explanation
Indices: 1208912--1208984 Score: 110
Period size: 23 Copynumber: 3.2 Consensus size: 23
1208902 ATACTTTACA
1208912 ATATAAGCACTACCTATTACATT
1 ATATAAGCACTACCTATTACATT
**
1208935 ATATAAAAACTACCTATTACATT
1 ATATAAGCACTACCTATTACATT
* *
1208958 ATATAAGCGCTACCTATTACATC
1 ATATAAGCACTACCTATTACATT
1208981 ATAT
1 ATAT
1208985 TTTTACCTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.41, C:0.21, G:0.04, T:0.34
Consensus pattern (23 bp):
ATATAAGCACTACCTATTACATT
Found at i:1209028 original size:22 final size:22
Alignment explanation
Indices: 1209002--1209046 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
1208992 TATTATATTG
1209002 AAAGTATCCATACTTTTTATAA
1 AAAGTATCCATACTTTTTATAA
* *
1209024 AAAGTATCGATACTTTTTTTAA
1 AAAGTATCCATACTTTTTATAA
1209046 A
1 A
1209047 GTTATGTCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.40, C:0.11, G:0.07, T:0.42
Consensus pattern (22 bp):
AAAGTATCCATACTTTTTATAA
Found at i:1209437 original size:23 final size:23
Alignment explanation
Indices: 1209401--1209473 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
1209391 ATACTTTACA
* *
1209401 ATATAAGCACTACCTATTACATT
1 ATATAAACGCTACCTATTACATT
*
1209424 ATATAAACGTTACCTATTACATT
1 ATATAAACGCTACCTATTACATT
* *
1209447 ATATAAGCGCTACCTATTACATC
1 ATATAAACGCTACCTATTACATT
1209470 ATAT
1 ATAT
1209474 TTTTACCTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.36
Consensus pattern (23 bp):
ATATAAACGCTACCTATTACATT
Found at i:1209629 original size:487 final size:486
Alignment explanation
Indices: 1208512--1209770 Score: 2313
Period size: 487 Copynumber: 2.6 Consensus size: 486
1208502 TTATAATATG
1208512 TTGAAAGTGTCCATACTTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGT
1 TTGAAAGTGTCCATAC-TTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGT
*
1208577 TTTAATTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCAC
65 TTCAATTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCAC
1208642 AAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATT
130 AAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATT
*
1208707 AACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAAAAATATATA
195 AACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATA
* *
1208772 TCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTC
260 CCGTAACGTAAAAAATAAATCATTAAACGCCTATAATTACTAAATTAATATCTTAAAACTCACTC
1208837 AAAAGATAACCTTAAATTAATGTTTTCACAGTGAAAAAGTATGGACACTTTTATAAAAAAGATAG
325 AAAAGATAACCTTAAATTAATGTTTTCACAGTGAAAAAGTATGGACACTTTTATAAAAAAGATAG
1208902 ATACTTTACAATATAAGCACTACCTATTACATTATATAAAAACTACCTATTACATTATATAAGCG
390 ATACTTTACAATATAAGCACTACCTATTACATTATATAAAAACTACCTATTACATTATATAAGCG
1208967 CTACCTATTACATCATATTTTTACCTATTATA
455 CTACCTATTACATCATATTTTTACCTATTATA
* * *
1208999 TTGAAAGTATCCATACTTTTTATAAAAAGTATCGATACTTTTTTTAAAGTTATGTCATTTATGTT
1 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
1209064 TCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCAC
66 TCAA-TTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCAC
1209129 AAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATT
130 AAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATT
**
1209194 AACCAAAGATAATAATAAATATGTAATATATATGTTTATTAATTTTAATTTAATAATAATATATA
195 AACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATA
*
1209259 CCGTAACGTAAAACATAAATCATTAAACGCCTATAATTACTAAATTAATATCTTAAAACTCACTC
260 CCGTAACGTAAAAAATAAATCATTAAACGCCTATAATTACTAAATTAATATCTTAAAACTCACTC
*
1209324 AAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAATGAT
325 AAAAGATAACCTTAAATTAATGTTTT-CACAGTG-AAAAAGTATGGACACTTTTATAAAAAAGAT
***
1209389 AGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGTTACCTATTACATTATATAAG
388 AGATACTTTACAATATAAGCACTACCTATTACATTATATAAAAACTACCTATTACATTATATAAG
1209454 CGCTACCTATTACATCATATTTTTACCTATTATA
453 CGCTACCTATTACATCATATTTTTACCTATTATA
1209488 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
1209553 TCAATTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCACA
66 TCAATTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCACA
*
1209618 AAAAA-TATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAAAAATATTA
131 AAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATTA
*
1209682 ACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATGATAATATATAC
196 ACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATAC
* *
1209747 CATAACATAAAAAATAAATCATTA
261 CGTAACGTAAAAAATAAATCATTA
1209771 GATACACAAA
Statistics
Matches: 745, Mismatches: 24, Indels: 6
0.96 0.03 0.01
Matches are distributed among these distances:
486 50 0.07
487 431 0.58
488 73 0.10
489 191 0.26
ACGTcount: A:0.41, C:0.11, G:0.07, T:0.41
Consensus pattern (486 bp):
TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
TCAATTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCACA
AAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATTA
ACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATAC
CGTAACGTAAAAAATAAATCATTAAACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCA
AAAGATAACCTTAAATTAATGTTTTCACAGTGAAAAAGTATGGACACTTTTATAAAAAAGATAGA
TACTTTACAATATAAGCACTACCTATTACATTATATAAAAACTACCTATTACATTATATAAGCGC
TACCTATTACATCATATTTTTACCTATTATA
Found at i:1211095 original size:183 final size:183
Alignment explanation
Indices: 1210787--1211541 Score: 1322
Period size: 183 Copynumber: 4.1 Consensus size: 183
1210777 TACTTAAAAT
1210787 TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
1 TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
1210852 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGT
66 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGT
1210917 CGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
131 CGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
1210970 TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
1 TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
1211035 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGT
66 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGT
*
1211100 CGACACTTTTTGACAATGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
131 CGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
* **
1211153 TACCGTCACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAATTGGTATA
1 TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
*
1211218 TTTATACCGGTTATATTATAAAATTATCTATT--ATTATAATTCTGGGTTCCGATGTGTAAATGT
66 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGT
1211281 CGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
131 CGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
* *
1211334 TACCGACACAATATTAAAAAGTGTCGATATAGATTATAGACCTATTCGCTCATAAAACCGGTATA
1 TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
* * *
1211399 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTTTTTTCAA
66 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATG---TGTAAA
* *
1211464 --TCGACACTTTTTGA-ACTGGTATCGACACATTTTTCTTCCATTCTGGACATAAAG
128 TGTCGACACTTTTTGACA-AGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
*
1211518 TACAGACACAATATTAAAAAGTGT
1 TACCGACACAATATTAAAAAGTGT
1211542 GAAAACTTTG
Statistics
Matches: 548, Mismatches: 18, Indels: 11
0.95 0.03 0.02
Matches are distributed among these distances:
181 174 0.32
183 297 0.54
184 73 0.13
186 4 0.01
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (183 bp):
TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
TTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGT
CGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
Found at i:1212768 original size:12 final size:12
Alignment explanation
Indices: 1212751--1212847 Score: 122
Period size: 12 Copynumber: 7.8 Consensus size: 12
1212741 CTTGTTTGGA
*
1212751 TCATCGTCAGCT
1 TCATCGTCATCT
1212763 TCATCGTCATCATCT
1 TCATCG---TCATCT
*
1212778 TCATCGTCAGCT
1 TCATCGTCATCT
*
1212790 TCATCGTCATCA
1 TCATCGTCATCT
1212802 TCATCGTCATCT
1 TCATCGTCATCT
1212814 TCATCGTCATCT
1 TCATCGTCATCT
*
1212826 TCATCGTCAGCT
1 TCATCGTCATCT
*
1212838 TCATCTTCAT
1 TCATCGTCAT
1212848 TGACCGCTTG
Statistics
Matches: 74, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
12 63 0.85
15 11 0.15
ACGTcount: A:0.19, C:0.33, G:0.10, T:0.38
Consensus pattern (12 bp):
TCATCGTCATCT
Found at i:1212781 original size:6 final size:6
Alignment explanation
Indices: 1212772--1212847 Score: 80
Period size: 6 Copynumber: 12.7 Consensus size: 6
1212762 TTCATCGTCA
* * * * * *
1212772 TCATCT TCATCG TCAGCT TCATCG TCATCA TCATCG TCATCT TCATCG
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT
* *
1212820 TCATCT TCATCG TCAGCT TCATCT TCAT
1 TCATCT TCATCT TCATCT TCATCT TCAT
1212848 TGACCGCTTG
Statistics
Matches: 56, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
6 56 1.00
ACGTcount: A:0.18, C:0.33, G:0.09, T:0.39
Consensus pattern (6 bp):
TCATCT
Found at i:1212805 original size:24 final size:24
Alignment explanation
Indices: 1212750--1212847 Score: 142
Period size: 24 Copynumber: 4.0 Consensus size: 24
1212740 ACTTGTTTGG
1212750 ATCATCGTCAGCTTCATCGTCATC
1 ATCATCGTCAGCTTCATCGTCATC
1212774 ATCTTCATCGTCAGCTTCATCGTCATC
1 A---TCATCGTCAGCTTCATCGTCATC
*
1212801 ATCATCGTCATCTTCATCGTCATC
1 ATCATCGTCAGCTTCATCGTCATC
* *
1212825 TTCATCGTCAGCTTCATCTTCAT
1 ATCATCGTCAGCTTCATCGTCAT
1212848 TGACCGCTTG
Statistics
Matches: 67, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
24 43 0.64
27 24 0.36
ACGTcount: A:0.19, C:0.33, G:0.10, T:0.38
Consensus pattern (24 bp):
ATCATCGTCAGCTTCATCGTCATC
Found at i:1214862 original size:198 final size:199
Alignment explanation
Indices: 1214365--1215100 Score: 1237
Period size: 198 Copynumber: 3.7 Consensus size: 199
1214355 TTATATACCA
* * *
1214365 ATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTAAAAAATTACCTATTACATTCTACTT
1 ATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTT
* * *
1214430 ATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGGTCGACACTTTATTGTTGCACCA
66 TTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCA
* *
1214495 TGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTAAAAAAAGTATCGACACATTATTT
131 TGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT-ACAAAAGTGTCGACACATTATTT
1214560 AGACT
195 AGACT
*
1214565 ATTATCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTT
1 ATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTT
* *
1214630 TTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACACTTTGTGGTTGCACCC
66 TTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCA
*
1214695 TGTTTGCCATTCATTCTGGACCAAAAATATCGACACGAACTACAAAAGTGTCGACACATTATTTA
131 TGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTACAAAAGTGTCGACACATTATTTA
1214760 GA-T
196 GACT
1214763 ATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTT
1 ATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTT
*
1214828 TTGGTTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCAGCC
66 TTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCA-CC
* * * *
1214893 -TGTTTGCCATTCATTCTGGACCATAAATATCGACACAAAGTACAAAAGCGTCGATACATTATTT
130 ATGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTACAAAAGTGTCGACACATTATTT
1214957 AGACCT
195 AGA-CT
* * *
1214963 ATTCTCTCATAAAACCGGTATACTTGCACCGATTAGATTGAAAAA-TACCTATTACATTATACTT
1 ATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTT
1215027 TTGGGTTTCGATGTTT-TGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCA
66 TTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCA
1215091 TGTTTGCCAT
131 TGTTTGCCAT
1215101 ATTGTAAATT
Statistics
Matches: 508, Mismatches: 24, Indels: 10
0.94 0.04 0.02
Matches are distributed among these distances:
197 2 0.00
198 242 0.48
199 59 0.12
200 205 0.40
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.36
Consensus pattern (199 bp):
ATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTT
TTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCA
TGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTACAAAAGTGTCGACACATTATTTA
GACT
Found at i:1215224 original size:18 final size:18
Alignment explanation
Indices: 1215201--1215261 Score: 59
Period size: 19 Copynumber: 3.3 Consensus size: 18
1215191 TCTCATTCAT
*
1215201 AATTATATTCACATACAA
1 AATTATAATCACATACAA
**
1215219 AATTATAAATCGTATACAA
1 AATTAT-AATCACATACAA
**
1215238 AATTATAAATCTTATACAA
1 AATTAT-AATCACATACAA
1215257 AATTA
1 AATTA
1215262 ACCCTACATT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
18 6 0.16
19 32 0.84
ACGTcount: A:0.52, C:0.11, G:0.02, T:0.34
Consensus pattern (18 bp):
AATTATAATCACATACAA
Found at i:1215237 original size:19 final size:19
Alignment explanation
Indices: 1215213--1215261 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
1215203 TTATATTCAC
1215213 ATACAAAATTATAAATCGT
1 ATACAAAATTATAAATCGT
*
1215232 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
1215251 ATACAAAATTA
1 ATACAAAATTA
1215262 ACCCTACATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.55, C:0.10, G:0.02, T:0.33
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:1216314 original size:32 final size:33
Alignment explanation
Indices: 1216255--1216319 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
1216245 CATCTTAATA
*
1216255 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
* *
1216288 TCACCCCTCAACA-CTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
1216320 CCATCTATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.23, C:0.48, G:0.00, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCACT
Found at i:1216378 original size:21 final size:21
Alignment explanation
Indices: 1216353--1216417 Score: 94
Period size: 21 Copynumber: 3.1 Consensus size: 21
1216343 CCCCTTATGC
* *
1216353 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
*
1216374 CTCTCAAGTTTCTATTCGACT
1 CTCTCAAGTTTCTCTTCGACT
*
1216395 CTATCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
1216416 CT
1 CT
1216418 TGATTGTCTT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.18, C:0.29, G:0.11, T:0.42
Consensus pattern (21 bp):
CTCTCAAGTTTCTCTTCGACT
Found at i:1218651 original size:17 final size:18
Alignment explanation
Indices: 1218629--1218671 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
1218619 ATATATCCGG
1218629 TATCATTT-TACCGGTTT
1 TATCATTTATACCGGTTT
1218646 TATCATTTTGATACCGGTTT
1 TATCA-TTT-ATACCGGTTT
1218666 TATCAT
1 TATCAT
1218672 ATTTTTACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.22
18 3 0.13
19 1 0.04
20 14 0.61
ACGTcount: A:0.21, C:0.16, G:0.12, T:0.51
Consensus pattern (18 bp):
TATCATTTATACCGGTTT
Found at i:1218680 original size:20 final size:19
Alignment explanation
Indices: 1218634--1218692 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 19
1218624 TCCGGTATCA
1218634 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
1218653 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
* *
1218674 TTTTACCTGTTATATCATT
1 TTTTACCGGTTTTATCATT
1218693 GTGGATCGAT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
19 3 0.09
20 28 0.82
21 3 0.09
ACGTcount: A:0.20, C:0.15, G:0.10, T:0.54
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:1218846 original size:20 final size:20
Alignment explanation
Indices: 1218815--1218861 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
1218805 TCTGGTAATG
1218815 TTTTACCAGTTTTATCAT-T
1 TTTTACCAGTTTTATCATAT
*
1218834 TTGTTACCGGTTTTATCATAT
1 TT-TTACCAGTTTTATCATAT
1218855 TTTTACC
1 TTTTACC
1218862 TGGTATATCT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 2 0.08
20 20 0.80
21 3 0.12
ACGTcount: A:0.19, C:0.17, G:0.09, T:0.55
Consensus pattern (20 bp):
TTTTACCAGTTTTATCATAT
Found at i:1218905 original size:181 final size:180
Alignment explanation
Indices: 1218601--1219073 Score: 644
Period size: 181 Copynumber: 2.6 Consensus size: 180
1218591 CGTACTTACG
* *
1218601 AAAGTATCGACACTTTCAATATATCCGGTATCATTTTACCGGTTTTATCATTTTGATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCTGGTAT-GTTTTACCGGTTTTATCATTTTGATACCGGTTT
* *
1218666 TATCATATTTTTACCTGTTATATCATTGTGGATCGATATATATTTTTAAAGTATCGACACATTAT
65 TATCATATTTTTACCTGTTATATCATTTTGGATCGATACAT-TTTTTAAAGTATCGACACATTAT
*
1218731 AGGCGCTAAAACTGATTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-T
129 AGGAGCTAAAACTGATTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
* *
1218782 AAAGTATCGACACTTTCAATATATCTGGTAATGTTTTACCAGTTTTATCATTTTGTTACCGGTTT
1 AAAGTATCGACACTTTCAATATATCTGGT-ATGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * *
1218847 TATCATATTTTTACCTGGTATATCTTTTTGGATCGATACATTTTTTAAAAGTATCGACACTTTAT
65 TATCATATTTTTACCTGTTATATCATTTTGGATCGATACATTTTTT-AAAGTATCGACACATTAT
** * * *
1218912 AGGATTTAAAACTGCTTCTCTTTTAAATTCACGAAGTGTCTATCCTTATATT
129 AGGAGCTAAAACTGATTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
* * * **
1218964 AAAGTACCGACACTTTAAATGTATCTGGTA-GCTCTTTACCGGTTTTATCATTTCAATACCGGTT
1 AAAGTATCGACACTTTCAATATATCTGGTATG-T-TTTACCGGTTTTATCATTTTGATACCGGTT
* * * * * *
1219028 TTGTCATAGTTTTACATGTTATATCGTTTTGGATCAACACATTTTT
64 TTATCATATTTTTACCTGTTATATCATTTTGGATCGATACATTTTT
1219074 AATTTGGATC
Statistics
Matches: 258, Mismatches: 29, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
180 6 0.02
181 158 0.61
182 94 0.36
ACGTcount: A:0.28, C:0.16, G:0.13, T:0.43
Consensus pattern (180 bp):
AAAGTATCGACACTTTCAATATATCTGGTATGTTTTACCGGTTTTATCATTTTGATACCGGTTTT
ATCATATTTTTACCTGTTATATCATTTTGGATCGATACATTTTTTAAAGTATCGACACATTATAG
GAGCTAAAACTGATTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
Found at i:1219295 original size:5 final size:5
Alignment explanation
Indices: 1219285--1219309 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
1219275 ATTAGTTACA
1219285 GATTT GATTT GATTT GATTT GATTT
1 GATTT GATTT GATTT GATTT GATTT
1219310 TCAGTTTAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.20, T:0.60
Consensus pattern (5 bp):
GATTT
Found at i:1230384 original size:30 final size:30
Alignment explanation
Indices: 1230348--1230461 Score: 144
Period size: 30 Copynumber: 3.8 Consensus size: 30
1230338 CGAAGGACTG
* * *
1230348 GTCCATAGGTCTCGAATAACCTAGGTAAT-T
1 GTCCATATGTCTCGAAGAACATAGGT-ATCT
1230378 GTCCATATGT-TCAGAAGAACATAGGTATCT
1 GTCCATATGTCTC-GAAGAACATAGGTATCT
*
1230408 GTCCATATGTCCCGAAGAACATAGGTATCT
1 GTCCATATGTCTCGAAGAACATAGGTATCT
1230438 GTCCATATGTC-CTGAAGAACATAG
1 GTCCATATGTCTC-GAAGAACATAG
1230462 ATAACCCTCG
Statistics
Matches: 76, Mismatches: 4, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
29 5 0.07
30 70 0.92
31 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (30 bp):
GTCCATATGTCTCGAAGAACATAGGTATCT
Found at i:1231332 original size:20 final size:20
Alignment explanation
Indices: 1231307--1231344 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1231297 AGATTACGTA
1231307 GGGGGTA-CAGATTCCCCCAT
1 GGGGGTATC-GATTCCCCCAT
1231327 GGGGGTATCGATTCCCCC
1 GGGGGTATCGATTCCCCC
1231345 TAAATAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 16 0.94
21 1 0.06
ACGTcount: A:0.16, C:0.32, G:0.32, T:0.21
Consensus pattern (20 bp):
GGGGGTATCGATTCCCCCAT
Found at i:1235262 original size:14 final size:15
Alignment explanation
Indices: 1235234--1235262 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1235224 TGTGAAAAGG
1235234 AATAGTAGATGTGTA
1 AATAGTAGATGTGTA
1235249 AATAGTAG-TGTGTA
1 AATAGTAGATGTGTA
1235263 TAAGTAAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.38, C:0.00, G:0.28, T:0.34
Consensus pattern (15 bp):
AATAGTAGATGTGTA
Found at i:1239479 original size:22 final size:21
Alignment explanation
Indices: 1239437--1239480 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
1239427 TTATGGAGTA
*
1239437 CTGTAGCAGGGTATCGATTCC
1 CTGTAGCAGGGAATCGATTCC
*
1239458 CTGTAGCAGGGGAATCGGTTCC
1 CTGTAGCA-GGGAATCGATTCC
1239480 C
1 C
1239481 CTTTTTGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.18, C:0.25, G:0.32, T:0.25
Consensus pattern (21 bp):
CTGTAGCAGGGAATCGATTCC
Found at i:1239580 original size:32 final size:34
Alignment explanation
Indices: 1239523--1239587 Score: 100
Period size: 32 Copynumber: 2.0 Consensus size: 34
1239513 TACTGTAGCA
1239523 GGTATTGTTCATCACTGTTTATTACTGTTCATAT
1 GGTATTGTTCATCACTGTTTATTACTGTTCATAT
1239557 GGTATTGTTCAT-AC-GTATT-TTACTGTTCATA
1 GGTATTGTTCATCACTGT-TTATTACTGTTCATA
1239588 AATACATTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
32 14 0.47
33 4 0.13
34 12 0.40
ACGTcount: A:0.22, C:0.14, G:0.15, T:0.49
Consensus pattern (34 bp):
GGTATTGTTCATCACTGTTTATTACTGTTCATAT
Found at i:1240095 original size:22 final size:23
Alignment explanation
Indices: 1240070--1240113 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
1240060 AATTAAGTTT
1240070 TAATATTA-AAA-TAATTTCAAAA
1 TAATATTACAAAGT-ATTTCAAAA
*
1240092 TAATTTTACAAAGTATTTCAAA
1 TAATATTACAAAGTATTTCAAA
1240114 CCATTTCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 7 0.37
23 11 0.58
24 1 0.05
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.39
Consensus pattern (23 bp):
TAATATTACAAAGTATTTCAAAA
Found at i:1246286 original size:23 final size:22
Alignment explanation
Indices: 1246243--1246324 Score: 78
Period size: 23 Copynumber: 3.7 Consensus size: 22
1246233 ATAGGGCTGA
* *
1246243 GGGAATCGATACCCCCATGAAG
1 GGGAACCGATACCCCCTTGAAG
* *
1246265 GGGAACCGATTCCCCCTTTGAAT
1 GGGAACCGATACCCCC-TTGAAG
*
1246288 GGGAACCGATTCCCCCCTT--AG
1 GGGAACCGA-TACCCCCTTGAAG
*
1246309 GGGAATCGATACCCCC
1 GGGAACCGATACCCCC
1246325 AAGGGTTCTG
Statistics
Matches: 50, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
20 6 0.12
21 9 0.18
22 14 0.28
23 15 0.30
24 6 0.12
ACGTcount: A:0.24, C:0.33, G:0.24, T:0.18
Consensus pattern (22 bp):
GGGAACCGATACCCCCTTGAAG
Found at i:1247913 original size:18 final size:18
Alignment explanation
Indices: 1247892--1247932 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
1247882 AGAATAACAT
1247892 GAGGAACAAGCACGAG-CA
1 GAGGAACAAGCAC-AGCCA
1247910 GAGGAACAAGCACAGCCA
1 GAGGAACAAGCACAGCCA
1247928 GAGGA
1 GAGGA
1247933 TCAAATGCCT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 2 0.09
18 20 0.91
ACGTcount: A:0.44, C:0.22, G:0.34, T:0.00
Consensus pattern (18 bp):
GAGGAACAAGCACAGCCA
Found at i:1250017 original size:34 final size:34
Alignment explanation
Indices: 1249972--1250051 Score: 133
Period size: 34 Copynumber: 2.4 Consensus size: 34
1249962 ACCAAGCTTG
1249972 GGTATCGATACCCAAATTGCATTCGAAGTTTTAA
1 GGTATCGATACCCAAATTGCATTCGAAGTTTTAA
* **
1250006 GGTATCAATACCCAAATTGCATTCGAAGTTTTTT
1 GGTATCGATACCCAAATTGCATTCGAAGTTTTAA
1250040 GGTATCGATACC
1 GGTATCGATACC
1250052 TCCCTTATGG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 42 1.00
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (34 bp):
GGTATCGATACCCAAATTGCATTCGAAGTTTTAA
Found at i:1252603 original size:25 final size:25
Alignment explanation
Indices: 1252575--1252622 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
1252565 TTCAATATAG
*
1252575 TTCTT-ATTCGTTTTTCTAGTTTTTT
1 TTCTTCATT-GTTTTTATAGTTTTTT
*
1252600 TTCTTCATTTTTTTTATAGTTTT
1 TTCTTCATTGTTTTTATAGTTTT
1252623 GAAATTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 17 0.85
26 3 0.15
ACGTcount: A:0.10, C:0.10, G:0.06, T:0.73
Consensus pattern (25 bp):
TTCTTCATTGTTTTTATAGTTTTTT
Found at i:1255893 original size:45 final size:46
Alignment explanation
Indices: 1255842--1255933 Score: 177
Period size: 45 Copynumber: 2.0 Consensus size: 46
1255832 AAATTGCGAG
1255842 AAGTACAAATACATAATTTCATGAAAAAGTCCACTTATG-TATTTT
1 AAGTACAAATACATAATTTCATGAAAAAGTCCACTTATGTTATTTT
1255887 AAGTACAAATACATAATTTCATGAAAAAGTCCACTTATGTTATTTT
1 AAGTACAAATACATAATTTCATGAAAAAGTCCACTTATGTTATTTT
1255933 A
1 A
1255934 CTTCAAATTA
Statistics
Matches: 46, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
45 39 0.85
46 7 0.15
ACGTcount: A:0.42, C:0.13, G:0.09, T:0.36
Consensus pattern (46 bp):
AAGTACAAATACATAATTTCATGAAAAAGTCCACTTATGTTATTTT
Found at i:1257245 original size:101 final size:101
Alignment explanation
Indices: 1257070--1257271 Score: 404
Period size: 101 Copynumber: 2.0 Consensus size: 101
1257060 TCTTCTCAGA
1257070 AAGGTCAGGAAAAACTTTTTGAATATCGAGTATCTTGAAATGTTATAACCAATTGAAAGCATGGA
1 AAGGTCAGGAAAAACTTTTTGAATATCGAGTATCTTGAAATGTTATAACCAATTGAAAGCATGGA
1257135 TTTGATCTAAAAATAAAAAAGAGATGAAATCATTTT
66 TTTGATCTAAAAATAAAAAAGAGATGAAATCATTTT
1257171 AAGGTCAGGAAAAACTTTTTGAATATCGAGTATCTTGAAATGTTATAACCAATTGAAAGCATGGA
1 AAGGTCAGGAAAAACTTTTTGAATATCGAGTATCTTGAAATGTTATAACCAATTGAAAGCATGGA
1257236 TTTGATCTAAAAATAAAAAAGAGATGAAATCATTTT
66 TTTGATCTAAAAATAAAAAAGAGATGAAATCATTTT
1257272 TTGTTTGTAG
Statistics
Matches: 101, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
101 101 1.00
ACGTcount: A:0.44, C:0.09, G:0.17, T:0.31
Consensus pattern (101 bp):
AAGGTCAGGAAAAACTTTTTGAATATCGAGTATCTTGAAATGTTATAACCAATTGAAAGCATGGA
TTTGATCTAAAAATAAAAAAGAGATGAAATCATTTT
Found at i:1263047 original size:29 final size:27
Alignment explanation
Indices: 1263014--1263112 Score: 67
Period size: 29 Copynumber: 3.4 Consensus size: 27
1263004 CTATATCTCT
1263014 CATTCTAAATTGATCCATAAACTTTTGAA
1 CATTCTAAATT-ATCC-TAAACTTTTGAA
* * *
1263043 CATTCCAATTTCATCCTCAAA-TTATGACTCA
1 CATTCTAAATT-ATCCT-AAACTTTTGA---A
*
1263074 TATTCTAAATTAGTCCCTAAACTTTTGAA
1 CATTCTAAATTA-T-CCTAAACTTTTGAA
1263103 CATTC-AAATT
1 CATTCTAAATT
1263113 CCATACTCAA
Statistics
Matches: 54, Mismatches: 9, Indels: 15
0.69 0.12 0.19
Matches are distributed among these distances:
28 11 0.20
29 21 0.39
30 1 0.02
31 13 0.24
32 8 0.15
ACGTcount: A:0.35, C:0.21, G:0.05, T:0.38
Consensus pattern (27 bp):
CATTCTAAATTATCCTAAACTTTTGAA
Found at i:1263140 original size:60 final size:59
Alignment explanation
Indices: 1262998--1263167 Score: 182
Period size: 60 Copynumber: 2.8 Consensus size: 59
1262988 ATCATACATT
* * * * *
1262998 CTCAAACTATATCTCTCATTCTAAATTGATCCATAAACTTTTGAACATTCCAATTTCATC
1 CTCAAACTATAACTCTCATTCTAAATTG-TCCCTAAACTTTTGAACATTCAAATTCCATA
* *
1263058 CTCAAATTATGACTCAT-ATTCTAAATTAGTCCCTAAACTTTTGAACATTCAAATTCCATA
1 CTCAAACTATAACTC-TCATTCTAAATT-GTCCCTAAACTTTTGAACATTCAAATTCCATA
* * **
1263118 CTCAAACTACAACTCTCGTTCTAAATTGGTTTCTAATA-TTTTGAACATTC
1 CTCAAACTATAACTCTCATTCTAAATT-GTCCCTAA-ACTTTTGAACATTC
1263168 CGATAGCATC
Statistics
Matches: 92, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
59 1 0.01
60 88 0.96
61 3 0.03
ACGTcount: A:0.34, C:0.23, G:0.05, T:0.38
Consensus pattern (59 bp):
CTCAAACTATAACTCTCATTCTAAATTGTCCCTAAACTTTTGAACATTCAAATTCCATA
Found at i:1263242 original size:29 final size:29
Alignment explanation
Indices: 1263188--1263243 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
1263178 CCCCTTAATC
**
1263188 ATTCAAAAGTTTAGGGATGAAAATAGAGA
1 ATTCAAAAGTTTAGGGACCAAAATAGAGA
* *
1263217 ATTCAAAAGTTTGGGGACCAATATAGA
1 ATTCAAAAGTTTAGGGACCAAAATAGA
1263244 ATGAGGGTCA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.45, C:0.07, G:0.23, T:0.25
Consensus pattern (29 bp):
ATTCAAAAGTTTAGGGACCAAAATAGAGA
Found at i:1263304 original size:60 final size:61
Alignment explanation
Indices: 1263218--1263344 Score: 150
Period size: 60 Copynumber: 2.1 Consensus size: 61
1263208 AAATAGAGAA
** * * *
1263218 TTCAAAAGTTTGGGGACCAATATAGAATGAGGGTCACATTTTGGGGATGA-ATTTGGAATG-
1 TTCAAAAGTTTGAAGACCAATATAGAATGAGGATCACAGTTTGGGGATGACA-TTAGAATGT
* * * *
1263278 TTCAAAAGTTTGAAGATCAATTTAGAATGATGATCATAGTTTGGGGATGACATTAGAATGT
1 TTCAAAAGTTTGAAGACCAATATAGAATGAGGATCACAGTTTGGGGATGACATTAGAATGT
1263339 TTCAAA
1 TTCAAA
1263345 GTTCAAGGGC
Statistics
Matches: 56, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
60 49 0.88
61 7 0.12
ACGTcount: A:0.35, C:0.08, G:0.25, T:0.32
Consensus pattern (61 bp):
TTCAAAAGTTTGAAGACCAATATAGAATGAGGATCACAGTTTGGGGATGACATTAGAATGT
Found at i:1266337 original size:184 final size:184
Alignment explanation
Indices: 1266028--1266395 Score: 736
Period size: 184 Copynumber: 2.0 Consensus size: 184
1266018 CAAAGGTGAA
1266028 CTATAGTCATTCAATTTTAGGTTCTATAGAGATTATGCGTTAGATTTTAAAATACTTCAATTTAA
1 CTATAGTCATTCAATTTTAGGTTCTATAGAGATTATGCGTTAGATTTTAAAATACTTCAATTTAA
1266093 ATATTGAACTTTAGTTTGGATTCAATTAGAGAATCGAGCCATTAAATCATTGATAATATGATGAC
66 ATATTGAACTTTAGTTTGGATTCAATTAGAGAATCGAGCCATTAAATCATTGATAATATGATGAC
1266158 ATGATCTTTCTTTCTCATTTTGCTATAGAAAATTATCAATTTTTCCGGTCGTAG
131 ATGATCTTTCTTTCTCATTTTGCTATAGAAAATTATCAATTTTTCCGGTCGTAG
1266212 CTATAGTCATTCAATTTTAGGTTCTATAGAGATTATGCGTTAGATTTTAAAATACTTCAATTTAA
1 CTATAGTCATTCAATTTTAGGTTCTATAGAGATTATGCGTTAGATTTTAAAATACTTCAATTTAA
1266277 ATATTGAACTTTAGTTTGGATTCAATTAGAGAATCGAGCCATTAAATCATTGATAATATGATGAC
66 ATATTGAACTTTAGTTTGGATTCAATTAGAGAATCGAGCCATTAAATCATTGATAATATGATGAC
1266342 ATGATCTTTCTTTCTCATTTTGCTATAGAAAATTATCAATTTTTCCGGTCGTAG
131 ATGATCTTTCTTTCTCATTTTGCTATAGAAAATTATCAATTTTTCCGGTCGTAG
1266396 TTGCTGCTCA
Statistics
Matches: 184, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
184 184 1.00
ACGTcount: A:0.32, C:0.12, G:0.14, T:0.41
Consensus pattern (184 bp):
CTATAGTCATTCAATTTTAGGTTCTATAGAGATTATGCGTTAGATTTTAAAATACTTCAATTTAA
ATATTGAACTTTAGTTTGGATTCAATTAGAGAATCGAGCCATTAAATCATTGATAATATGATGAC
ATGATCTTTCTTTCTCATTTTGCTATAGAAAATTATCAATTTTTCCGGTCGTAG
Found at i:1271209 original size:75 final size:75
Alignment explanation
Indices: 1271058--1271265 Score: 283
Period size: 75 Copynumber: 2.8 Consensus size: 75
1271048 CAAAGCCAAA
* * **
1271058 AATTCCAGATTGCTCAGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTGAATGGT
1 AATTCCAGAATGCTCAGAGGGAACCGATT-CCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
1271123 TTGGCTCCGAG
65 TTGGCTCCGAG
* *
1271134 ATTTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTT
1 AATTCCAGAATGCTCAGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTT
* *
1271199 TTGTTCCGAG
66 TGGCTCCGAG
* * * *
1271209 AATTCCAGTATGCTCAGAGGGAACCGATCCCCCCCA-AGGGGGTACCGATTCCCCCCT
1 AATTCCAGAATGCTCAGAGGGAACCGAT-TCCCCCATAGGAGGAACCGATTCCCCCCT
1271266 GTTCAACGGT
Statistics
Matches: 117, Mismatches: 14, Indels: 3
0.87 0.10 0.02
Matches are distributed among these distances:
75 85 0.73
76 32 0.27
ACGTcount: A:0.24, C:0.32, G:0.24, T:0.21
Consensus pattern (75 bp):
AATTCCAGAATGCTCAGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTT
TGGCTCCGAG
Found at i:1278918 original size:9 final size:8
Alignment explanation
Indices: 1278896--1278946 Score: 52
Period size: 9 Copynumber: 6.2 Consensus size: 8
1278886 TGTTTCAACA
1278896 TTTTGGAT
1 TTTTGGAT
1278904 ATTTTGGAT
1 -TTTTGGAT
1278913 TGTTT-GAT
1 T-TTTGGAT
1278921 TTTGTGGAT
1 TTT-TGGAT
*
1278930 TGTTGGA-
1 TTTTGGAT
1278937 TTTTGGAT
1 TTTTGGAT
1278945 TT
1 TT
1278947 ATGAATGGTG
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
7 8 0.22
8 12 0.33
9 16 0.44
ACGTcount: A:0.14, C:0.00, G:0.27, T:0.59
Consensus pattern (8 bp):
TTTTGGAT
Found at i:1278930 original size:17 final size:17
Alignment explanation
Indices: 1278898--1278941 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
1278888 TTTCAACATT
1278898 TTGGATATTT-TGGATTG
1 TTGGAT-TTTGTGGATTG
*
1278915 TTTGATTTTGTGGATTG
1 TTGGATTTTGTGGATTG
1278932 TTGGATTTTG
1 TTGGATTTTG
1278942 GATTTATGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 3 0.12
17 21 0.88
ACGTcount: A:0.14, C:0.00, G:0.30, T:0.57
Consensus pattern (17 bp):
TTGGATTTTGTGGATTG
Found at i:1279654 original size:75 final size:75
Alignment explanation
Indices: 1279565--1279732 Score: 212
Period size: 75 Copynumber: 2.2 Consensus size: 75
1279555 TTGCTCAGAG
** * * *
1279565 GGAACCGATTCCCCCCTGAATGGTTTGGCTCCGAGATTTCCAGAATGCTCAGAGGGAACTGAT-T
1 GGAACCGATTCCCCCCTGAACAGTTTGGCTCCGAGAATTCCAGAATGCTCAGAGGGAACCGATCC
1279629 CCCCCATAGGA
66 CCCCCA-AGGA
* * * * *
1279640 GGAACCGATTCCCCCCTAAACAGTTTTGTTCCGAGAATTCCAGTATGCTCGGAGGGAACCGATCC
1 GGAACCGATTCCCCCCTGAACAGTTTGGCTCCGAGAATTCCAGAATGCTCAGAGGGAACCGATCC
*
1279705 CCCCCAAGGG
66 CCCCCAAGGA
*
1279715 GGTACCGATTCCCCCCTG
1 GGAACCGATTCCCCCCTG
1279733 TTCAACGGTC
Statistics
Matches: 79, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
75 73 0.92
76 6 0.08
ACGTcount: A:0.23, C:0.32, G:0.24, T:0.21
Consensus pattern (75 bp):
GGAACCGATTCCCCCCTGAACAGTTTGGCTCCGAGAATTCCAGAATGCTCAGAGGGAACCGATCC
CCCCCAAGGA
Found at i:1284403 original size:20 final size:20
Alignment explanation
Indices: 1284374--1284424 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
1284364 AATGTATTTT
*
1284374 GTGCACCGATGCACAAGTA-A
1 GTGCATCGATGCAC-AGTATA
* *
1284394 GTGCATCGATACACTGTATA
1 GTGCATCGATGCACAGTATA
1284414 GTGCATCGATG
1 GTGCATCGATG
1284425 AATACCTTCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
19 3 0.12
20 23 0.88
ACGTcount: A:0.29, C:0.22, G:0.25, T:0.24
Consensus pattern (20 bp):
GTGCATCGATGCACAGTATA
Found at i:1285028 original size:28 final size:27
Alignment explanation
Indices: 1284996--1285052 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 27
1284986 ACAAGTTAAA
1284996 TGACATATGA-ATATGAATCATATGAAAG
1 TGACATAT-ACATATGAAT-ATATGAAAG
* *
1285024 TGACATGTACATGTGAATATATGAAAG
1 TGACATATACATATGAATATATGAAAG
1285051 TG
1 TG
1285053 TGATAACATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 12 0.46
28 14 0.54
ACGTcount: A:0.42, C:0.07, G:0.21, T:0.30
Consensus pattern (27 bp):
TGACATATACATATGAATATATGAAAG
Found at i:1285166 original size:31 final size:31
Alignment explanation
Indices: 1285128--1285192 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
1285118 AGAGTCGAGG
*
1285128 GTTTACCTATGTTC-TAAGGAACATATGGACA
1 GTTTACCTAGGTTCTTAAGG-ACATATGGACA
* *
1285159 GTTTACCTAGGTTCTTCAGGACCTATGGACA
1 GTTTACCTAGGTTCTTAAGGACATATGGACA
1285190 GTT
1 GTT
1285193 ACCGAGGATC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
31 26 0.87
32 4 0.13
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (31 bp):
GTTTACCTAGGTTCTTAAGGACATATGGACA
Found at i:1285280 original size:30 final size:30
Alignment explanation
Indices: 1285151--1285280 Score: 170
Period size: 30 Copynumber: 4.3 Consensus size: 30
1285141 CTAAGGAACA
* * * * *
1285151 TATGGACAGTTTACCTAGGTTCTTCAGGACC
1 TATGGATAG-TTACCGAGGATCTTTATGACC
*
1285182 TATGGACAGTTACCGAGGATCTTTATGACC
1 TATGGATAGTTACCGAGGATCTTTATGACC
*
1285212 TTTGGATAGTTACCGAGGATCTTTATGACC
1 TATGGATAGTTACCGAGGATCTTTATGACC
* *
1285242 TCTAGATAGTTACCGAGGATCTTTATGACC
1 TATGGATAGTTACCGAGGATCTTTATGACC
1285272 TATGGATAG
1 TATGGATAG
1285281 GTCCTTCGGG
Statistics
Matches: 89, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
30 80 0.90
31 9 0.10
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.33
Consensus pattern (30 bp):
TATGGATAGTTACCGAGGATCTTTATGACC
Found at i:1290420 original size:11 final size:12
Alignment explanation
Indices: 1290394--1290418 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1290384 TATAAACTTG
1290394 AACTAAAAAAAA
1 AACTAAAAAAAA
1290406 AACTAAAAAAAA
1 AACTAAAAAAAA
1290418 A
1 A
1290419 CTCAAGGAGC
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:0.84, C:0.08, G:0.00, T:0.08
Consensus pattern (12 bp):
AACTAAAAAAAA
Found at i:1292439 original size:45 final size:45
Alignment explanation
Indices: 1292375--1292465 Score: 157
Period size: 45 Copynumber: 2.0 Consensus size: 45
1292365 CTCCCGCCAG
1292375 AGCCCATAAAAATTTTATAATTTTTATACTATATA-ATTTTTAAGC
1 AGCCCATAAAAATTTTATAA-TTTTATACTATATATATTTTTAAGC
*
1292420 AGCCCATAAAAGTTTTATAATTTTATACTATATATATTTTTAAGC
1 AGCCCATAAAAATTTTATAATTTTATACTATATATATTTTTAAGC
1292465 A
1 A
1292466 TAGACACATC
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
44 14 0.32
45 30 0.68
ACGTcount: A:0.40, C:0.11, G:0.05, T:0.44
Consensus pattern (45 bp):
AGCCCATAAAAATTTTATAATTTTATACTATATATATTTTTAAGC
Found at i:1299428 original size:20 final size:20
Alignment explanation
Indices: 1299400--1299448 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
1299390 TTTTCTTATC
*
1299400 TACTGTTTATAATTAGTAAT
1 TACTATTTATAATTAGTAAT
1299420 TACTATTTATAATTAGTAAT
1 TACTATTTATAATTAGTAAT
1299440 TACTATTTA
1 TACTATTTA
1299449 CTACTATAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.37, C:0.06, G:0.06, T:0.51
Consensus pattern (20 bp):
TACTATTTATAATTAGTAAT
Found at i:1310788 original size:230 final size:229
Alignment explanation
Indices: 1310344--1310858 Score: 582
Period size: 230 Copynumber: 2.2 Consensus size: 229
1310334 GAAAAACTCG
* * * * * * *
1310344 TCAACTCGAATTTACCATGGATCTTTGACATATAAAAGCTATCATCTTAGTCCAAAAAGACTGCA
1 TCAACTCGAATTCACCATAGATATTCGACACATAAAAGCTATCATCTTAGTCCAAAAAGACCGAA
* * * *
1310409 TTTTCGGTGTTGAACTGCATATACACAGCAATTAAAGAAACCGAAGACGATAACTAATTTATCAA
66 TTTTCGATGTCGAACTGCATATACACAGCAATTAAAGAAACCAAAGACGATAACTAATTAATCAA
* *
1310474 TATAAAGAGATGGCAAAACACCCTTTACATTGAAGTAGGGAAGAACTGTATATACTAATCATCAA
131 TATAAAGAGATGACAAAACACCCTTTACATTGAAGTAGGGAAGAACTGTATATACTAATAATCAA
* * *
1310539 GTAAAGAAAATCCCCCCATCAATTCAATTAGATCA
196 GGAAAGAAAA-CACCCCATCAATCCAATTAGATCA
* * *
1310574 TCAACTCGAATTCACCATAGATATTCGACACATGAAAGCTATCATCTTAGTTC-AGAAGACCGAA
1 TCAACTCGAATTCACCATAGATATTCGACACATAAAAGCTATCATCTTAGTCCAAAAAGACCGAA
** * * *
1310638 TTTTCGATGTCGAACTGCATATGTATAGCAGTTCATAA-AAGCCAAAG-CTGATAACTAATTAAT
66 TTTTCGATGTCGAACTGCATATACACAGCAATT-A-AAGAAACCAAAGAC-GATAACTAATTAAT
1310701 CAA-ATGCAAAGAGATGACAAAACACCCTTTCACATTGAAGT-GGAGAAGAACTGTATATACTAA
128 CAATAT--AAAGAGATGACAAAACACCCTTT-ACATTGAAGTAGG-GAAGAACTGTATATACTAA
**
1310764 TAATTGAGGAAAGAAAA-ACCCCATCAATCCAATTAG---A
189 TAATCAAGGAAAGAAAACACCCCATCAATCCAATTAGATCA
* * ** * *
1310801 TCAACTC-AATTTCACCATATATCTTTAACAAATGAAAAGCTATCATTTTAGTCCAAAA
1 TCAACTCGAA-TTCACCATAGATATTCGACACAT-AAAAGCTATCATCTTAGTCCAAAA
1310859 GACTTTTTTT
Statistics
Matches: 240, Mismatches: 35, Indels: 21
0.81 0.12 0.07
Matches are distributed among these distances:
226 2 0.01
227 26 0.11
228 17 0.07
229 40 0.17
230 87 0.36
231 26 0.11
232 42 0.17
ACGTcount: A:0.41, C:0.19, G:0.14, T:0.26
Consensus pattern (229 bp):
TCAACTCGAATTCACCATAGATATTCGACACATAAAAGCTATCATCTTAGTCCAAAAAGACCGAA
TTTTCGATGTCGAACTGCATATACACAGCAATTAAAGAAACCAAAGACGATAACTAATTAATCAA
TATAAAGAGATGACAAAACACCCTTTACATTGAAGTAGGGAAGAACTGTATATACTAATAATCAA
GGAAAGAAAACACCCCATCAATCCAATTAGATCA
Found at i:1314555 original size:29 final size:28
Alignment explanation
Indices: 1314509--1314564 Score: 103
Period size: 29 Copynumber: 2.0 Consensus size: 28
1314499 ACTAAAAGGA
1314509 CATTCACCATTCCTCTTCTATAATAACT
1 CATTCACCATTCCTCTTCTATAATAACT
1314537 CATTCACCACTTCCTCTTCTATAATAAC
1 CATTCACCA-TTCCTCTTCTATAATAAC
1314565 CTTAATCATC
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
28 9 0.33
29 18 0.67
ACGTcount: A:0.29, C:0.34, G:0.00, T:0.38
Consensus pattern (28 bp):
CATTCACCATTCCTCTTCTATAATAACT
Found at i:1316228 original size:22 final size:20
Alignment explanation
Indices: 1316203--1316243 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
1316193 AGAGTTATGA
*
1316203 TTTATTTATATAATATAATTTT
1 TTTAATTATAT-ATA-AATTTT
1316225 TTTAATTATATATAAATTT
1 TTTAATTATATATAAATTT
1316244 AAAGTTGTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 3 0.17
22 10 0.56
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
TTTAATTATATATAAATTTT
Found at i:1316865 original size:15 final size:15
Alignment explanation
Indices: 1316821--1316866 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
1316811 ATTAAGTTAT
1316821 AAAAAATAT-AAAT-
1 AAAAAATATAAAATA
* *
1316834 GAAAAATATAATTATA
1 AAAAAATATAA-AATA
1316850 AAAAAATATAAAATA
1 AAAAAATATAAAATA
1316865 AA
1 AA
1316867 TTTAAAAGCT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
13 8 0.31
14 1 0.04
15 7 0.27
16 10 0.38
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (15 bp):
AAAAAATATAAAATA
Found at i:1319490 original size:44 final size:45
Alignment explanation
Indices: 1319367--1319497 Score: 210
Period size: 45 Copynumber: 2.9 Consensus size: 45
1319357 AATTTTGTAT
* * *
1319367 CAATATATTTACCATTTATCCCATAAGCTCTTAAGCTTATTTTAC
1 CAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTAC
*
1319412 CAATATACTTACTATTTATTCCATAAGCTCGTAAGCTTATTTTAC
1 CAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTAC
*
1319457 CAATATACTTGCCA-TTATTCCATAAGCTCGTAAGCTTATTT
1 CAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
1319498 GCATGCTTAT
Statistics
Matches: 80, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
44 27 0.34
45 53 0.66
ACGTcount: A:0.31, C:0.21, G:0.07, T:0.41
Consensus pattern (45 bp):
CAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTAC
Found at i:1326046 original size:23 final size:24
Alignment explanation
Indices: 1325989--1326048 Score: 65
Period size: 22 Copynumber: 2.7 Consensus size: 24
1325979 TATAGCATGA
1325989 GGAATCGATA--CCCCCTTGAAGG
1 GGAATCGATATCCCCCCTTGAAGG
* * *
1326011 GGAACCAAT-TCCCCCCTTGGA-G
1 GGAATCGATATCCCCCCTTGAAGG
1326033 GGAATCGATATCCCCC
1 GGAATCGATATCCCCC
1326049 ACGGGGTCTG
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
22 15 0.50
23 15 0.50
ACGTcount: A:0.25, C:0.33, G:0.23, T:0.18
Consensus pattern (24 bp):
GGAATCGATATCCCCCCTTGAAGG
Found at i:1329561 original size:27 final size:26
Alignment explanation
Indices: 1329483--1329566 Score: 71
Period size: 27 Copynumber: 3.1 Consensus size: 26
1329473 TTATCACATT
1329483 TTGACAAGTCAAATTCAACTTCAAAA
1 TTGACAAGTCAAATTCAACTTCAAAA
* ** * *
1329509 TCTAACACCTCATATCTCTTAA-TTCAATCA
1 T-TGACAAGTCAAAT-TC--AACTTCAA-AA
1329539 TTGACAAGTCAAATTCAACTTCAAAA
1 TTGACAAGTCAAATTCAACTTCAAAA
1329565 TT
1 TT
1329567 TACTAACTCC
Statistics
Matches: 42, Mismatches: 10, Indels: 12
0.66 0.16 0.19
Matches are distributed among these distances:
26 6 0.14
27 14 0.33
28 4 0.10
29 14 0.33
30 4 0.10
ACGTcount: A:0.40, C:0.23, G:0.05, T:0.32
Consensus pattern (26 bp):
TTGACAAGTCAAATTCAACTTCAAAA
Found at i:1330258 original size:3 final size:3
Alignment explanation
Indices: 1330246--1330307 Score: 60
Period size: 3 Copynumber: 21.7 Consensus size: 3
1330236 AGATTATTTA
* *
1330246 TAT T-T TAT TAT TAT TAT TAT AAT TA- TAT T-T ATAT TAT AAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT
*
1330289 AAT TAT TA- TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TA
1330308 AATAATTTTA
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
2 7 0.15
3 40 0.83
4 1 0.02
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:1330258 original size:17 final size:17
Alignment explanation
Indices: 1330238--1330322 Score: 64
Period size: 17 Copynumber: 5.5 Consensus size: 17
1330228 TCATTTGAAG
* *
1330238 ATTATTTATATTTTATT
1 ATTATTTATATATAATT
1330255 ATTA-TTAT-TATAATT
1 ATTATTTATATATAATT
1330270 A-TATTTATATTATAATT
1 ATTATTTATA-TATAATT
*
1330287 A-TAATTAT-TAT-ATT
1 ATTATTTATATATAATT
1330301 ATTA-TTA-A-ATAATT
1 ATTATTTATATATAATT
1330315 -TTATTTAT
1 ATTATTTAT
1330323 TTACTATTAC
Statistics
Matches: 57, Mismatches: 3, Indels: 18
0.73 0.04 0.23
Matches are distributed among these distances:
13 5 0.09
14 15 0.26
15 15 0.26
16 4 0.07
17 18 0.32
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
ATTATTTATATATAATT
Found at i:1330263 original size:20 final size:19
Alignment explanation
Indices: 1330238--1330306 Score: 59
Period size: 20 Copynumber: 3.3 Consensus size: 19
1330228 TCATTTGAAG
1330238 ATTATTTATATTTTATTATT
1 ATTATTTATATTTTA-TATT
1330258 ATTATTATAATTATATTTATATT
1 ATTATT-T-A-TAT-TTTATATT
*
1330281 A-TAATTATAATTATTATATT
1 ATTATTTAT-ATT-TTATATT
1330301 ATTATT
1 ATTATT
1330307 AAATAATTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 13
0.73 0.04 0.24
Matches are distributed among these distances:
19 2 0.05
20 17 0.43
21 5 0.12
22 4 0.10
23 8 0.20
24 4 0.10
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
ATTATTTATATTTTATATT
Found at i:1330287 original size:26 final size:25
Alignment explanation
Indices: 1330243--1330307 Score: 85
Period size: 26 Copynumber: 2.5 Consensus size: 25
1330233 TGAAGATTAT
* *
1330243 TTATATTTTATTATTATTATTATAA
1 TTATATTTTATTATAATTATAATAA
*
1330268 TTATATTTATATTATAATTATAATTA
1 TTATATTT-TATTATAATTATAATAA
1330294 TTATATTATTATTA
1 TTATATT-TTATTA
1330308 AATAATTTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
25 8 0.23
26 26 0.74
27 1 0.03
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (25 bp):
TTATATTTTATTATAATTATAATAA
Found at i:1330322 original size:20 final size:20
Alignment explanation
Indices: 1330247--1330323 Score: 59
Period size: 20 Copynumber: 3.6 Consensus size: 20
1330237 GATTATTTAT
*
1330247 ATTTTA-TTATTATTATTATA
1 ATTTTATTTATTATTA-AATA
*
1330267 ATTATATTTA-TATTATAATTATA
1 ATTTTATTTATTA-T-TAA--ATA
1330290 ATTATTATATTATTATTAAATA
1 ATT-TTAT-TTATTATTAAATA
1330312 ATTTTATTTATT
1 ATTTTATTTATT
1330324 TACTATTACA
Statistics
Matches: 46, Mismatches: 3, Indels: 16
0.71 0.05 0.25
Matches are distributed among these distances:
20 12 0.26
21 8 0.17
22 8 0.17
23 6 0.13
24 6 0.13
25 4 0.09
26 2 0.04
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
ATTTTATTTATTATTAAATA
Found at i:1330801 original size:12 final size:12
Alignment explanation
Indices: 1330784--1330813 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
1330774 GAAAAACACC
1330784 AACAAACCACAA
1 AACAAACCACAA
1330796 AACAAACCACAA
1 AACAAACCACAA
1330808 AACAAA
1 AACAAA
1330814 AAGAGAAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.70, C:0.30, G:0.00, T:0.00
Consensus pattern (12 bp):
AACAAACCACAA
Found at i:1331836 original size:38 final size:36
Alignment explanation
Indices: 1331794--1331878 Score: 95
Period size: 34 Copynumber: 2.3 Consensus size: 36
1331784 TTACTATTAT
*
1331794 TATTTATTATTTATGTCAATATATATATATATAAATAA
1 TATTTATTATTTA-GTC-ATATAAATATATATAAATAA
*
1331832 TATTTATCTA---AGTCTTATAAATATATATAAATAA
1 TATTTAT-TATTTAGTCATATAAATATATATAAATAA
1331866 TATTTATTTATTT
1 TATTTA-TTATTT
1331879 TATGAAAATA
Statistics
Matches: 40, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
34 26 0.65
35 4 0.10
36 1 0.03
38 7 0.17
39 2 0.05
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.52
Consensus pattern (36 bp):
TATTTATTATTTAGTCATATAAATATATATAAATAA
Found at i:1332179 original size:11 final size:13
Alignment explanation
Indices: 1332142--1332181 Score: 50
Period size: 11 Copynumber: 3.3 Consensus size: 13
1332132 TGTTTAATAA
1332142 AATATA-TATATT
1 AATATATTATATT
*
1332154 AATATATTATCTT
1 AATATATTATATT
1332167 AA-A-ATTATATT
1 AATATATTATATT
1332178 AATA
1 AATA
1332182 AACTTAACAG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 9 0.38
12 8 0.33
13 7 0.29
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (13 bp):
AATATATTATATT
Found at i:1332648 original size:24 final size:22
Alignment explanation
Indices: 1332609--1332663 Score: 58
Period size: 24 Copynumber: 2.5 Consensus size: 22
1332599 TTATATATAC
*
1332609 TTATTATTTTCCTAATATTTATA
1 TTATTATTTTACTAATATTT-TA
* *
1332632 TATATTATTTTATTAATGTTTTA
1 T-TATTATTTTACTAATATTTTA
1332655 TT-TTATTTT
1 TTATTATTTT
1332664 CAAGTATTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
21 7 0.25
22 1 0.04
23 4 0.14
24 16 0.57
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (22 bp):
TTATTATTTTACTAATATTTTA
Found at i:1337990 original size:10 final size:10
Alignment explanation
Indices: 1337967--1338008 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
1337957 TCATCCAGCA
*
1337967 AAGAAAGAAG
1 AAGAAAAAAG
1337977 AAGAAGAAAA-
1 AAGAA-AAAAG
1337987 AAGAAAAAAG
1 AAGAAAAAAG
*
1337997 ATGAAAAAAG
1 AAGAAAAAAG
1338007 AA
1 AA
1338009 AAATGGGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
9 4 0.15
10 20 0.74
11 3 0.11
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.02
Consensus pattern (10 bp):
AAGAAAAAAG
Found at i:1338002 original size:17 final size:17
Alignment explanation
Indices: 1337977--1338011 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
1337967 AAGAAAGAAG
1337977 AAGAAGAAAAAAGAAAA
1 AAGAAGAAAAAAGAAAA
*
1337994 AAGATGAAAAAAGAAAA
1 AAGAAGAAAAAAGAAAA
1338011 A
1 A
1338012 TGGGAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (17 bp):
AAGAAGAAAAAAGAAAA
Found at i:1338018 original size:16 final size:17
Alignment explanation
Indices: 1337977--1338021 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
1337967 AAGAAAGAAG
*
1337977 AAGAAGAAAAAAGAAAA
1 AAGAGGAAAAAAGAAAA
*
1337994 AAGATGAAAAAAGAAAA
1 AAGAGGAAAAAAGAAAA
*
1338011 ATG-GGAAAAAA
1 AAGAGGAAAAAA
1338022 AGGGAAAAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
16 7 0.28
17 18 0.72
ACGTcount: A:0.76, C:0.00, G:0.20, T:0.04
Consensus pattern (17 bp):
AAGAGGAAAAAAGAAAA
Found at i:1338028 original size:26 final size:26
Alignment explanation
Indices: 1337990--1338041 Score: 79
Period size: 25 Copynumber: 2.0 Consensus size: 26
1337980 AAGAAAAAAG
*
1337990 AAAAAAGATGAAAAAAGAAAAATGGGA
1 AAAAAAGA-GGAAAAAGAAAAATGGGA
1338017 AAAAAAG-GGAAAAAGAAAAATGGGA
1 AAAAAAGAGGAAAAAGAAAAATGGGA
1338042 GAAATTGAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 17 0.71
27 7 0.29
ACGTcount: A:0.69, C:0.00, G:0.25, T:0.06
Consensus pattern (26 bp):
AAAAAAGAGGAAAAAGAAAAATGGGA
Found at i:1340388 original size:114 final size:114
Alignment explanation
Indices: 1340188--1340407 Score: 377
Period size: 114 Copynumber: 1.9 Consensus size: 114
1340178 CACGTTCTCG
*
1340188 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTT
1 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTC
* * * *
1340253 GGTATGAACCCTAAAACCAATCATTGGATTTGAAAGATGAATTTGCTCA
66 GGTAGGAACCCCAAAACCAATCATTGGAATTAAAAGATGAATTTGCTCA
*
1340302 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTC
1 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTC
*
1340367 GGTAGGAACCCCAGAACCAATCATTGGAATTAAAAGATGAA
66 GGTAGGAACCCCAAAACCAATCATTGGAATTAAAAGATGAA
1340408 CTGCATGATC
Statistics
Matches: 99, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
114 99 1.00
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.30
Consensus pattern (114 bp):
TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTC
GGTAGGAACCCCAAAACCAATCATTGGAATTAAAAGATGAATTTGCTCA
Found at i:1342520 original size:46 final size:46
Alignment explanation
Indices: 1342445--1342533 Score: 133
Period size: 46 Copynumber: 1.9 Consensus size: 46
1342435 CTGACTAGAA
* * * *
1342445 ATCTGTGCATAAGTCACATGAAATAATGAATGTGTTGTCAAATAGC
1 ATCTGTGCAGAAGCCACAGGAAAGAATGAATGTGTTGTCAAATAGC
*
1342491 ATCTGTGCAGAAGCCACAGGAAAGGATGAATGTGTTGTCAAAT
1 ATCTGTGCAGAAGCCACAGGAAAGAATGAATGTGTTGTCAAAT
1342534 GTTTTACTAG
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 38 1.00
ACGTcount: A:0.36, C:0.13, G:0.24, T:0.27
Consensus pattern (46 bp):
ATCTGTGCAGAAGCCACAGGAAAGAATGAATGTGTTGTCAAATAGC
Found at i:1342546 original size:54 final size:54
Alignment explanation
Indices: 1342487--1342594 Score: 135
Period size: 54 Copynumber: 2.0 Consensus size: 54
1342477 TGTTGTCAAA
* * * **
1342487 TAGCATCTGTGCAGAAGCCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTAC
1 TAGCATCTGAGCAGAAACCACAGGAAAGGATGAATGTATTGAAAAATGTTTTAC
* * * *
1342541 TAGCATCTGAGCATAAACCACATGAGATGATGAATGTATTGAAAAATGTTTTAC
1 TAGCATCTGAGCAGAAACCACAGGAAAGGATGAATGTATTGAAAAATGTTTTAC
1342595 GAACCAGTCA
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
54 45 1.00
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (54 bp):
TAGCATCTGAGCAGAAACCACAGGAAAGGATGAATGTATTGAAAAATGTTTTAC
Found at i:1342994 original size:22 final size:22
Alignment explanation
Indices: 1342966--1343066 Score: 175
Period size: 22 Copynumber: 4.6 Consensus size: 22
1342956 ACATCTACAT
1342966 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
1342988 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
1343010 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
* *
1343032 TTTTTAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
*
1343054 TTTTCAAAGATGA
1 TCTTCAAAGATGA
1343067 AAGCTTTATT
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 76 1.00
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.39
Consensus pattern (22 bp):
TCTTCAAAGATGATAGATTCTC
Found at i:1343866 original size:76 final size:76
Alignment explanation
Indices: 1343737--1343907 Score: 288
Period size: 76 Copynumber: 2.2 Consensus size: 76
1343727 CTATTTCTCA
*
1343737 CATCTGTAAGTCCTACAATGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
1343802 AGCCTTAGGGT
66 AACCTTAGGGT
*
1343813 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGTTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
1343878 AACCTTTGGGT
66 AACCTTAGGGT
* *
1343889 CAGCTGTAAGCCCTACAGT
1 CATCTGTAAGTCCTACAGT
1343908 ACAGAAAGTT
Statistics
Matches: 89, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
76 89 1.00
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.34
Consensus pattern (76 bp):
CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AACCTTAGGGT
Found at i:1344226 original size:111 final size:112
Alignment explanation
Indices: 1343928--1344241 Score: 549
Period size: 112 Copynumber: 2.8 Consensus size: 112
1343918 TTTTTCTTAA
* *
1343928 AACATTTCCAGGTAGAGTTCATAATGAGAAGAACTCACCTGAAGAAGGAAGAAGAAGTTCATAAT
1 AACATTTCCA-GAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
* *
1343993 GAAAAGAACTTGTTCAACTTTTTGCTTGAATTCATCATTCGATGGATC
65 GAGAAGAACTTGTTCAACTTTTTGCTTGAATTCATCATTCAATGGATC
*
1344041 AACATTTCCAGAAGAGTTCATATTGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
1 AACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
1344106 AGAAGAACTTGTTCAACTTTTTGCTTGAATTCATCATTCAATGGATC
66 AGAAGAACTTGTTCAACTTTTTGCTTGAATTCATCATTCAATGGATC
*
1344153 AATATTTCCAGAAGA-TTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
1 AACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
*
1344217 AGAAGAACTTGTTCAACCTTTTGCT
66 AGAAGAACTTGTTCAACTTTTTGCT
1344242 CAACATTTCC
Statistics
Matches: 193, Mismatches: 8, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
111 72 0.37
112 111 0.58
113 10 0.05
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.28
Consensus pattern (112 bp):
AACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
AGAAGAACTTGTTCAACTTTTTGCTTGAATTCATCATTCAATGGATC
Found at i:1344263 original size:91 final size:90
Alignment explanation
Indices: 1344151--1344331 Score: 317
Period size: 91 Copynumber: 2.0 Consensus size: 90
1344141 ATTCAATGGA
*
1344151 TCAATATTTCCAGAAGATTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
1 TCAACATTTCCAGAAGATTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
1344216 GAGAAGAACTTGTTCAACCTTTTGC
66 GAGAAGAACTTGTTCAACCTTTTGC
* *
1344241 TCAACATTTCCAGAAGTGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAGGAAGTTCATAA
1 TCAACATTTCCAGAAG-ATTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAA
*
1344306 TGAGAAGAACTTGTTTAACCTTTTGC
65 TGAGAAGAACTTGTTCAACCTTTTGC
1344332 CTGAATCCAT
Statistics
Matches: 86, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
90 15 0.17
91 71 0.83
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27
Consensus pattern (90 bp):
TCAACATTTCCAGAAGATTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
GAGAAGAACTTGTTCAACCTTTTGC
Found at i:1344363 original size:112 final size:112
Alignment explanation
Indices: 1344241--1344961 Score: 982
Period size: 112 Copynumber: 6.5 Consensus size: 112
1344231 AACCTTTTGC
** *
1344241 TCAACATTTCCAGAAGTGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAGGAAGTTCATAA
1 TCAACATTTCCAGAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAA
*
1344306 TGAGAAGAACTTGTTTAACCTTTTGCCTGAATCCATCACTTGATGGA
66 TGAGAAGAACTTGTTCAACCTTTTGCCTGAATCCATCACTTGATGGA
* *
1344353 TCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAG-AGGAAGAAGAAATTCATA
1 TCAACATTTCCAGA-AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATA
* * *
1344417 TTGAGAAGAATTTGTTCAACCTTTTGCTTGAATCCATCACTTGATGGA
65 ATGAGAAGAACTTGTTCAACCTTTTGCCTGAATCCATCACTTGATGGA
**
1344465 TCAACATTTCCAGAAGTGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG-AGAAAGTTCATA
1 TCAACATTTCCAGAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG-AAGTTCATA
*
1344529 ATGAGAAGAACTTGTTTAACCTTTTG-CTCGAATCCATCACTTGATGGA
65 ATGAGAAGAACTTGTTCAACCTTTTGCCT-GAATCCATCACTTGATGGA
* *
1344577 TCAACATTTCCAGAAGTA-TTCATAATTAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATA
1 TCAACATTTCCAGAA-AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATA
* * *
1344641 ATGAGAAGAACTTGTTTAACTTTTTG-CTCGAATTCATCACTTGATGGA
65 ATGAGAAGAACTTGTTCAACCTTTTGCCT-GAATCCATCACTTGATGGA
* *
1344689 TCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAG-AGGAAGAAGAAATTCATA
1 TCAACATTTCCAGA-AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATA
* *
1344753 ATGAGAAGAATTTGTTCAACCTTTTGCCTGAATTCATCACTTGATGGA
65 ATGAGAAGAACTTGTTCAACCTTTTGCCTGAATCCATCACTTGATGGA
* * *
1344801 TTAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAATAAGAAGTTCATA
1 TCAACATTTCCAGA-AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATA
* ** * * *
1344866 ATGAGAAGAGCTTGTTCAACC-TTTGTTTG-ATGCTATCAC-AGAAGGA
65 ATGAGAAGAACTTGTTCAACCTTTTGCCTGAAT-CCATCACTTGATGGA
* *
1344912 --AATATTTTCCAG-AAAGTT-ATAATGAGAAGAACTCATATGAAGAAGGAAGA
1 TCAACA-TTTCCAGAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGA
1344962 GAATTTGTTC
Statistics
Matches: 551, Mismatches: 46, Indels: 29
0.88 0.07 0.05
Matches are distributed among these distances:
107 30 0.05
108 6 0.01
109 2 0.00
110 7 0.01
111 38 0.07
112 375 0.68
113 93 0.17
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.28
Consensus pattern (112 bp):
TCAACATTTCCAGAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAA
TGAGAAGAACTTGTTCAACCTTTTGCCTGAATCCATCACTTGATGGA
Found at i:1345208 original size:3 final size:3
Alignment explanation
Indices: 1345202--1345268 Score: 95
Period size: 3 Copynumber: 22.7 Consensus size: 3
1345192 TTCATTTGAA
1345202 TAT TAT T-T ATAT T-T TAT TAT TAT TAT TAT TAT TAT TAT TAAT TA-
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT
1345246 TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TA
1345269 AATAATTTTA
Statistics
Matches: 59, Mismatches: 0, Indels: 10
0.86 0.00 0.14
Matches are distributed among these distances:
2 5 0.08
3 50 0.85
4 4 0.07
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:1346026 original size:33 final size:33
Alignment explanation
Indices: 1345988--1346064 Score: 127
Period size: 33 Copynumber: 2.3 Consensus size: 33
1345978 GGCCACCGCA
*
1345988 CGGTGGCTGGCGGTGGTCATTACCACCGGAGCG
1 CGGTGGCCGGCGGTGGTCATTACCACCGGAGCG
* *
1346021 CGGTGGCCGGCGGTGGTCATTGCCACCTGAGCG
1 CGGTGGCCGGCGGTGGTCATTACCACCGGAGCG
1346054 CGGTGGCCGGC
1 CGGTGGCCGGC
1346065 ATGGTTGCCG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.09, C:0.30, G:0.44, T:0.17
Consensus pattern (33 bp):
CGGTGGCCGGCGGTGGTCATTACCACCGGAGCG
Found at i:1347165 original size:11 final size:13
Alignment explanation
Indices: 1347128--1347167 Score: 50
Period size: 11 Copynumber: 3.3 Consensus size: 13
1347118 TGTTTAATAA
1347128 AATATA-TATATT
1 AATATATTATATT
*
1347140 AATATATTATCTT
1 AATATATTATATT
1347153 AA-A-ATTATATT
1 AATATATTATATT
1347164 AATA
1 AATA
1347168 AACTTAGTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 9 0.38
12 8 0.33
13 7 0.29
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (13 bp):
AATATATTATATT
Found at i:1350883 original size:17 final size:19
Alignment explanation
Indices: 1350842--1350884 Score: 56
Period size: 17 Copynumber: 2.4 Consensus size: 19
1350832 AAATATAAGA
1350842 TTAAATTTAAAATTTAATG
1 TTAAATTTAAAATTTAATG
*
1350861 TT-AATTT-AAATTTCAT-
1 TTAAATTTAAAATTTAATG
1350877 TTAAATTT
1 TTAAATTT
1350885 TTATTATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 2 0.09
17 13 0.59
18 5 0.23
19 2 0.09
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (19 bp):
TTAAATTTAAAATTTAATG
Found at i:1362184 original size:16 final size:17
Alignment explanation
Indices: 1362146--1362193 Score: 71
Period size: 18 Copynumber: 2.8 Consensus size: 17
1362136 TGTTTATGAG
1362146 GGAATTAGAATCTGTGAA
1 GGAATTAGAATCTGT-AA
1362164 GGAATTAGAATCTGT-A
1 GGAATTAGAATCTGTAA
*
1362180 GGAATTGGAATCTG
1 GGAATTAGAATCTG
1362194 AATCTGAAAC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
16 14 0.48
18 15 0.52
ACGTcount: A:0.35, C:0.06, G:0.29, T:0.29
Consensus pattern (17 bp):
GGAATTAGAATCTGTAA
Found at i:1362826 original size:32 final size:32
Alignment explanation
Indices: 1362778--1362855 Score: 129
Period size: 32 Copynumber: 2.4 Consensus size: 32
1362768 AAACCCGAAT
*
1362778 CCGATCCGACCCGAATATCACACTTAAAAAAA
1 CCGACCCGACCCGAATATCACACTTAAAAAAA
* *
1362810 CCGACCCGACCTGAATATCACACTTAAAAAAC
1 CCGACCCGACCCGAATATCACACTTAAAAAAA
1362842 CCGACCCGACCCGA
1 CCGACCCGACCCGA
1362856 GCTCGATTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.38, C:0.37, G:0.12, T:0.13
Consensus pattern (32 bp):
CCGACCCGACCCGAATATCACACTTAAAAAAA
Found at i:1369707 original size:117 final size:117
Alignment explanation
Indices: 1369493--1369796 Score: 513
Period size: 117 Copynumber: 2.6 Consensus size: 117
1369483 CTAAGTCTTT
* *
1369493 GGGAAAGTGTGTGAAATGAATTGTGATTTTCAAAGTAGTAATTA-TGTTAGGTGAGAAAGTCAGA
1 GGGAAAGTGTGTGAAATGAATTGTGATTTTCCAAGTAGTAATTATTGGTAGGTGAGAAAGTCAGA
* *
1369557 AATTAGTACTCATTTCCTGGAAGTATGGTTGTAATTATTTGGGAAAGTTGAG
66 AATTAATACTCATTTCCTGGAAGTATGGTTGTAATTAGTTGGGAAAGTTGAG
*
1369609 GGGAAAGTGTGTGAAATGAATTGTGATTTTCCAAGTAGTAATTATTGGTAAGTGAGAAAGTCAGA
1 GGGAAAGTGTGTGAAATGAATTGTGATTTTCCAAGTAGTAATTATTGGTAGGTGAGAAAGTCAGA
* *
1369674 AATTAATATTCATTTCCTGGAAGTATGGTTGTAATTCGTTGGGAAAGTTGAG
66 AATTAATACTCATTTCCTGGAAGTATGGTTGTAATTAGTTGGGAAAGTTGAG
* *
1369726 GGGAAAGTGTGTGAAATGAATTGTGATCTTCCAAGTAGTAATTATTTGTAGGTGAG-AAGTCAGA
1 GGGAAAGTGTGTGAAATGAATTGTGATTTTCCAAGTAGTAATTATTGGTAGGTGAGAAAGTCAGA
1369790 AATTAAT
66 AATTAAT
1369797 TAATACTCAT
Statistics
Matches: 177, Mismatches: 10, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
116 58 0.33
117 119 0.67
ACGTcount: A:0.33, C:0.06, G:0.27, T:0.34
Consensus pattern (117 bp):
GGGAAAGTGTGTGAAATGAATTGTGATTTTCCAAGTAGTAATTATTGGTAGGTGAGAAAGTCAGA
AATTAATACTCATTTCCTGGAAGTATGGTTGTAATTAGTTGGGAAAGTTGAG
Found at i:1372747 original size:18 final size:18
Alignment explanation
Indices: 1372724--1372758 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1372714 TTCCATCCGG
*
1372724 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
1372742 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
1372759 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:1374115 original size:45 final size:45
Alignment explanation
Indices: 1374065--1374154 Score: 126
Period size: 45 Copynumber: 2.0 Consensus size: 45
1374055 CAAATGCAAC
*
1374065 AATTGAAAATGCATTGGACCCCACGACAATTTCAGCACCGAAAGT
1 AATTGAAAATGCATTGGACCCCACGACAATTGCAGCACCGAAAGT
* * * * *
1374110 AATTGATAATTCATTGGCCCCCACGGCAATTGCAGGACCGAAAGT
1 AATTGAAAATGCATTGGACCCCACGACAATTGCAGCACCGAAAGT
1374155 CACATTGGAC
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.21
Consensus pattern (45 bp):
AATTGAAAATGCATTGGACCCCACGACAATTGCAGCACCGAAAGT
Found at i:1374869 original size:28 final size:26
Alignment explanation
Indices: 1374829--1374881 Score: 88
Period size: 28 Copynumber: 2.0 Consensus size: 26
1374819 TGCATTCGAT
1374829 GAAGAAGAAGAGAGACATGGAGGAGGAG
1 GAAGAAGAAGAGAG--ATGGAGGAGGAG
1374857 GAAGAAGAAGAGAGATGGAGGAGGA
1 GAAGAAGAAGAGAGATGGAGGAGGA
1374882 AGATGAGAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 11 0.44
28 14 0.56
ACGTcount: A:0.47, C:0.02, G:0.47, T:0.04
Consensus pattern (26 bp):
GAAGAAGAAGAGAGATGGAGGAGGAG
Found at i:1374890 original size:28 final size:29
Alignment explanation
Indices: 1374826--1374891 Score: 84
Period size: 28 Copynumber: 2.3 Consensus size: 29
1374816 ACGTGCATTC
*
1374826 GATGAAGAAGAAGAGAGACATGGAGGAGGAG
1 GATG-AGAAGAAGAGAGA-ATGGAGGAGGAA
1374857 GA--AGAAGAAGAGAG-ATGGAGGAGGAA
1 GATGAGAAGAAGAGAGAATGGAGGAGGAA
1374883 GATGAGAAG
1 GATGAGAAG
1374892 GAGCAATAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
26 13 0.41
28 17 0.53
31 2 0.06
ACGTcount: A:0.47, C:0.02, G:0.45, T:0.06
Consensus pattern (29 bp):
GATGAGAAGAAGAGAGAATGGAGGAGGAA
Found at i:1379345 original size:44 final size:45
Alignment explanation
Indices: 1379278--1379366 Score: 117
Period size: 44 Copynumber: 2.0 Consensus size: 45
1379268 CAAATGCAAC
*
1379278 AATTGAAAATGCATTGGACCCCACGACAATTTCAGCACCGAAAGT
1 AATTGAAAATGCATTGGACCCCACGACAATTGCAGCACCGAAAGT
* * * * *
1379323 AATTGATAATTCA-TGGCCCCCACGGCAATTGCAGGACCGAAAGT
1 AATTGAAAATGCATTGGACCCCACGACAATTGCAGCACCGAAAGT
1379367 CACATTGGAC
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
44 27 0.71
45 11 0.29
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.20
Consensus pattern (45 bp):
AATTGAAAATGCATTGGACCCCACGACAATTGCAGCACCGAAAGT
Found at i:1380079 original size:28 final size:28
Alignment explanation
Indices: 1380039--1380093 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
1380029 TGCATTCGAT
1380039 GAAGAAGAAGAGAGACATGGAGGAGGAG
1 GAAGAAGAAGAGAGACATGGAGGAGGAG
*
1380067 GAAGAAGAAGAGAGATATGGAGGAGGA
1 GAAGAAGAAGAGAGACATGGAGGAGGA
1380094 AGATGAGAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.47, C:0.02, G:0.45, T:0.05
Consensus pattern (28 bp):
GAAGAAGAAGAGAGACATGGAGGAGGAG
Found at i:1381245 original size:21 final size:21
Alignment explanation
Indices: 1381203--1381246 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1381193 ATAAAAATAT
*
1381203 TAATTTACTAATTTCATAAAA
1 TAATTTACTAAATTCATAAAA
*
1381224 TAATATTACTAAATT-ATTAAA
1 TAAT-TTACTAAATTCATAAAA
1381245 TA
1 TA
1381247 TATAAAACAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (21 bp):
TAATTTACTAAATTCATAAAA
Found at i:1382133 original size:3 final size:3
Alignment explanation
Indices: 1382120--1382191 Score: 74
Period size: 3 Copynumber: 23.7 Consensus size: 3
1382110 CCCTTTTTTA
* * * * *
1382120 ATT AAT ATT ATT ATA ATT ATT AAT ATT ATTT CTT CTT -TCT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT AT-T ATT ATT
1382166 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
1382192 ATATAGAAAT
Statistics
Matches: 59, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
2 1 0.02
3 55 0.93
4 3 0.05
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:1382866 original size:2 final size:2
Alignment explanation
Indices: 1382861--1382885 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1382851 AGAAACGATA
1382861 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
1382886 CTATAAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1385163 original size:34 final size:34
Alignment explanation
Indices: 1385120--1385187 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
1385110 TCCATGGCGC
1385120 TCGAGGGAGAGACCGATAATACTAAATTATGATT
1 TCGAGGGAGAGACCGATAATACTAAATTATGATT
1385154 TCGAGGGAGAGACCGATAATACTAAATTATGATT
1 TCGAGGGAGAGACCGATAATACTAAATTATGATT
1385188 GCAAGTGTTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.38, C:0.12, G:0.24, T:0.26
Consensus pattern (34 bp):
TCGAGGGAGAGACCGATAATACTAAATTATGATT
Found at i:1385362 original size:21 final size:21
Alignment explanation
Indices: 1385299--1385362 Score: 51
Period size: 21 Copynumber: 3.0 Consensus size: 21
1385289 TTTGATTATT
*
1385299 TTTTTTATTA-ATTAAAA-AA
1 TTTTTAATTATATTAAAATAA
* * *
1385318 TAGTTTAAATTATTATTTAGATAA
1 T--TTTTAATTA-TATTAAAATAA
1385342 TTTTTAATTATATTAAAATAA
1 TTTTTAATTATATTAAAATAA
1385363 AAATTACTAA
Statistics
Matches: 33, Mismatches: 7, Indels: 8
0.69 0.15 0.17
Matches are distributed among these distances:
19 1 0.03
21 16 0.48
22 8 0.24
23 5 0.15
24 3 0.09
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (21 bp):
TTTTTAATTATATTAAAATAA
Found at i:1390298 original size:18 final size:18
Alignment explanation
Indices: 1390271--1390314 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
1390261 CCTCGTGCTT
1390271 CAATTCCCTCTTTCATTC
1 CAATTCCCTCTTTCATTC
*
1390289 CAATTTCCTCTTTCATTC
1 CAATTCCCTCTTTCATTC
1390307 CAATTCCC
1 CAATTCCC
1390315 AAATTACATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.18, C:0.39, G:0.00, T:0.43
Consensus pattern (18 bp):
CAATTCCCTCTTTCATTC
Found at i:1392478 original size:175 final size:176
Alignment explanation
Indices: 1392257--1392609 Score: 583
Period size: 175 Copynumber: 2.0 Consensus size: 176
1392247 ACATCTGTGC
*
1392257 AATGGTCTCTTAAAATGCCCTAATTTCTTATAAATCTTCTATAATATCCTGTCAACCCAAGAAAT
1 AATGGTCTCTTAAAATGCCATAATTTCTTATAAATCTTCTATAATATCCTGTCAACCCAAGAAAT
1392322 CCTCTAAGAGATTTAAAAGATTTAGGCTTGGGCCAAGC-GGCATAGCTTCCA-CCTTACTAGGGT
66 CCTCTAAGAGATTT-AAAGATTTAGGCTTGGGCCAAGCAGGC--A-CTTCCACCCTTACTAGGGT
1392385 CTG-GAAA-CCCTGCAGC-AGATAATATGACCTAGATACT-CACTTTAGT
127 CTGAGAAACCCCTGCAGCAAGATAATATGACCTAGATACTCCACTTTAGT
1392431 AATGGTCTCTTAATAATGCCATAATTTCTTATAAATCTTCTATAATATCCTGTCAACCCAAGAAA
1 AATGGTCTCTTAA-AATGCCATAATTTCTTATAAATCTTCTATAATATCCTGTCAACCCAAGAAA
*
1392496 TCCTCTAAGAGATTTAAAGATTTAGGCTTGGGCCAAGCATGCACTTCCACCCTTACTAGGGTCTG
65 TCCTCTAAGAGATTTAAAGATTTAGGCTTGGGCCAAGCAGGCACTTCCACCCTTACTAGGGTCTG
1392561 TAGAAACCCCTGCAGCAGAGATAATATGACCTAGATACTCCACTTTAGT
130 -AGAAACCCCTGCAGCA-AGATAATATGACCTAGATACTCCACTTTAGT
1392610 CTGACCAAAA
Statistics
Matches: 168, Mismatches: 2, Indels: 13
0.92 0.01 0.07
Matches are distributed among these distances:
172 6 0.04
173 16 0.10
174 36 0.21
175 71 0.42
176 9 0.05
178 21 0.12
179 9 0.05
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.30
Consensus pattern (176 bp):
AATGGTCTCTTAAAATGCCATAATTTCTTATAAATCTTCTATAATATCCTGTCAACCCAAGAAAT
CCTCTAAGAGATTTAAAGATTTAGGCTTGGGCCAAGCAGGCACTTCCACCCTTACTAGGGTCTGA
GAAACCCCTGCAGCAAGATAATATGACCTAGATACTCCACTTTAGT
Found at i:1397157 original size:98 final size:98
Alignment explanation
Indices: 1396988--1397176 Score: 261
Period size: 98 Copynumber: 1.9 Consensus size: 98
1396978 AGCTTGTTGC
* ** * *
1396988 AAAGATGGAGTGTCGACTTATTGTCATCAGAGATCCTGTTCGTTACCACCATTTCCAGAACGGAG
1 AAAGATGGAGTGTCGACTTATCGTCATCAGAGATCCAATTCGTCACCACCATTTCAAGAACGGAG
*
1397053 TATGTTCCTGTGGGGACTATTGGTAGCAAATGA
66 TATGTTCCTGTGGCGACTATTGGTAGCAAATGA
* * * * * *
1397086 AAAGATGGAGTTTTGACTTATCGTCATCAGAGATTCAATTTGTCACCGCCATTTCAAGAATGGAG
1 AAAGATGGAGTGTCGACTTATCGTCATCAGAGATCCAATTCGTCACCACCATTTCAAGAACGGAG
*
1397151 TATGTTCTTGTGGCGACTATTGGTAG
66 TATGTTCCTGTGGCGACTATTGGTAG
1397177 TCGTACGGCG
Statistics
Matches: 78, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
98 78 1.00
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.32
Consensus pattern (98 bp):
AAAGATGGAGTGTCGACTTATCGTCATCAGAGATCCAATTCGTCACCACCATTTCAAGAACGGAG
TATGTTCCTGTGGCGACTATTGGTAGCAAATGA
Found at i:1400550 original size:10 final size:10
Alignment explanation
Indices: 1400522--1400579 Score: 50
Period size: 10 Copynumber: 6.0 Consensus size: 10
1400512 TAGTTTAAAT
1400522 TAATAATTTAA
1 TAATAATTT-A
*
1400533 TGATAATTTA
1 TAATAATTTA
1400543 TAATAATTT-
1 TAATAATTTA
* *
1400552 TAA-AGTTAA
1 TAATAATTTA
*
1400561 T-ATGATTTA
1 TAATAATTTA
1400570 TAATAATTTA
1 TAATAATTTA
1400580 ATAAATATAA
Statistics
Matches: 36, Mismatches: 8, Indels: 7
0.71 0.16 0.14
Matches are distributed among these distances:
8 4 0.11
9 8 0.22
10 16 0.44
11 8 0.22
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.48
Consensus pattern (10 bp):
TAATAATTTA
Found at i:1405398 original size:16 final size:16
Alignment explanation
Indices: 1405377--1405409 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1405367 TTCAATGACT
1405377 TAACTTGGTGATAAAG
1 TAACTTGGTGATAAAG
1405393 TAACTTGGTGATAAAG
1 TAACTTGGTGATAAAG
1405409 T
1 T
1405410 TTGAGAGTAA
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:0.36, C:0.06, G:0.24, T:0.33
Consensus pattern (16 bp):
TAACTTGGTGATAAAG
Found at i:1408290 original size:21 final size:21
Alignment explanation
Indices: 1408264--1408305 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
1408254 CTACCCTTGC
1408264 TCAAACAGAGAGAATGAACGT
1 TCAAACAGAGAGAATGAACGT
1408285 TCAAACAGAGAGAATGAACGT
1 TCAAACAGAGAGAATGAACGT
1408306 GTTGCATGGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.48, C:0.14, G:0.24, T:0.14
Consensus pattern (21 bp):
TCAAACAGAGAGAATGAACGT
Found at i:1408368 original size:29 final size:29
Alignment explanation
Indices: 1408335--1408390 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
1408325 TCCCAACACA
*
1408335 TAGGTCGCCATGCCCTCCGGGCGACCTTG
1 TAGGTCGCCATGCACTCCGGGCGACCTTG
1408364 TAGGTCGCCATGCACTCCGGGCGACCT
1 TAGGTCGCCATGCACTCCGGGCGACCT
1408391 ACCCTCGCTC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.12, C:0.38, G:0.30, T:0.20
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCGGGCGACCTTG
Found at i:1408419 original size:10 final size:10
Alignment explanation
Indices: 1408406--1408454 Score: 53
Period size: 10 Copynumber: 4.6 Consensus size: 10
1408396 CGCTCGGCTT
1408406 CCCTCGGATG
1 CCCTCGGATG
*
1408416 CCCTCGCATAG
1 CCCTCGGAT-G
*
1408427 CTCGCTCGGTTG
1 C-C-CTCGGATG
1408439 CCCTCGGATG
1 CCCTCGGATG
1408449 CCCTCG
1 CCCTCG
1408455 CATAGCTCGT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
10 21 0.66
11 3 0.09
12 3 0.09
13 5 0.16
ACGTcount: A:0.08, C:0.43, G:0.27, T:0.22
Consensus pattern (10 bp):
CCCTCGGATG
Found at i:1408435 original size:33 final size:33
Alignment explanation
Indices: 1408394--1408484 Score: 130
Period size: 33 Copynumber: 2.8 Consensus size: 33
1408384 GCGACCTACC
1408394 CTCGCTCGGCTT-CCCTCGGATGCCCTCGCATAG
1 CTCGCTCGG-TTGCCCTCGGATGCCCTCGCATAG
1408427 CTCGCTCGGTTGCCCTCGGATGCCCTCGCATAG
1 CTCGCTCGGTTGCCCTCGGATGCCCTCGCATAG
* * * *
1408460 CTCGTTCGGATGGCCTCAGATGCCC
1 CTCGCTCGGTTGCCCTCGGATGCCC
1408485 AGCGTGTTGG
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
32 2 0.04
33 51 0.96
ACGTcount: A:0.10, C:0.40, G:0.26, T:0.24
Consensus pattern (33 bp):
CTCGCTCGGTTGCCCTCGGATGCCCTCGCATAG
Found at i:1408558 original size:29 final size:29
Alignment explanation
Indices: 1408521--1408578 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
1408511 GCAATCTCTT
* *
1408521 GTAGCTCGCCGGGAAGACATGGCGACCTA
1 GTAGCTCGCCCGAAAGACATGGCGACCTA
* *
1408550 GTAGGTCGCCCGAAAGGCATGGCGACCTA
1 GTAGCTCGCCCGAAAGACATGGCGACCTA
1408579 TGACCAACAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.24, C:0.28, G:0.34, T:0.14
Consensus pattern (29 bp):
GTAGCTCGCCCGAAAGACATGGCGACCTA
Found at i:1424076 original size:40 final size:40
Alignment explanation
Indices: 1424019--1424109 Score: 110
Period size: 40 Copynumber: 2.2 Consensus size: 40
1424009 CCATTTATTA
* * * * *
1424019 TGTATAAGTTGTGAATTTATTCCCTATATTTTAATTTGAT
1 TGTATAATTTGTAAATTTAGTACCTATATTTTAATTTAAT
*
1424059 TGTATAATTTGTAAATTTAGTATCTATATTTTAATTTAAT
1 TGTATAATTTGTAAATTTAGTACCTATATTTTAATTTAAT
1424099 TGAATATAATT
1 TG--TATAATT
1424110 ATTATATTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
40 36 0.84
42 7 0.16
ACGTcount: A:0.33, C:0.04, G:0.10, T:0.53
Consensus pattern (40 bp):
TGTATAATTTGTAAATTTAGTACCTATATTTTAATTTAAT
Found at i:1426709 original size:2 final size:2
Alignment explanation
Indices: 1426671--1426697 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1426661 AATTATTTGG
1426671 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1426698 CACACATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1433638 original size:15 final size:15
Alignment explanation
Indices: 1433589--1433640 Score: 77
Period size: 15 Copynumber: 3.5 Consensus size: 15
1433579 ATATTTGGAT
* *
1433589 GGGCGGGTGGATGTG
1 GGGCGGGCGGATGCG
*
1433604 GGGCAGGCGGATGCG
1 GGGCGGGCGGATGCG
1433619 GGGCGGGCGGATGCG
1 GGGCGGGCGGATGCG
1433634 GGGCGGG
1 GGGCGGG
1433641 TAATGTCTCA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 33 1.00
ACGTcount: A:0.08, C:0.15, G:0.67, T:0.10
Consensus pattern (15 bp):
GGGCGGGCGGATGCG
Found at i:1436528 original size:25 final size:24
Alignment explanation
Indices: 1436493--1436542 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 24
1436483 ATATATTTTA
*
1436493 TCGTCCCCTT-AAATTTTATAAAT
1 TCGTCCCCTTAAAATTTTAAAAAT
1436516 TCGTCCCTACTTAAAATTTTAAAAAT
1 TCGTCCC--CTTAAAATTTTAAAAAT
1436542 T
1 T
1436543 TACTTCCATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 7 0.30
25 3 0.13
26 13 0.57
ACGTcount: A:0.34, C:0.20, G:0.04, T:0.42
Consensus pattern (24 bp):
TCGTCCCCTTAAAATTTTAAAAAT
Found at i:1437246 original size:56 final size:56
Alignment explanation
Indices: 1437173--1437287 Score: 194
Period size: 56 Copynumber: 2.1 Consensus size: 56
1437163 TCAATGACCT
* * * *
1437173 TTTATTTTAATTGTTCGATCTAGTTTAGTTTGATTCAAGTTTTTCAGTCAAAGAAA
1 TTTATTTTAATTATTCGATCTAGTTTAGTTCGATTCAAGTATTTCAGTAAAAGAAA
1437229 TTTATTTTAATTATTCGATCTAGTTTAGTTCGATTCAAGTATTTCAGTAAAAGAAA
1 TTTATTTTAATTATTCGATCTAGTTTAGTTCGATTCAAGTATTTCAGTAAAAGAAA
1437285 TTT
1 TTT
1437288 TATCATATAA
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
56 55 1.00
ACGTcount: A:0.30, C:0.09, G:0.13, T:0.48
Consensus pattern (56 bp):
TTTATTTTAATTATTCGATCTAGTTTAGTTCGATTCAAGTATTTCAGTAAAAGAAA
Found at i:1437386 original size:26 final size:26
Alignment explanation
Indices: 1437356--1437407 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
1437346 TAATGCACCG
*
1437356 AAAGTGCATTAGTTGGCAGCAATGAT
1 AAAGTGCATTAGTTGGCAACAATGAT
1437382 AAAGTGCATTAGTTGGCAACAATGAT
1 AAAGTGCATTAGTTGGCAACAATGAT
1437408 TCATCAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.37, C:0.12, G:0.25, T:0.27
Consensus pattern (26 bp):
AAAGTGCATTAGTTGGCAACAATGAT
Found at i:1438236 original size:15 final size:18
Alignment explanation
Indices: 1438210--1438251 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
1438200 TCAAGCATCG
1438210 AGGAGAAGAAGACAGCTA
1 AGGAGAAGAAGACAGCTA
1438228 AGGAGAAGAAGACAGCTA
1 AGGAGAAGAAGACAGCTA
1438246 AGGAGA
1 AGGAGA
1438252 TATGAGATCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.50, C:0.10, G:0.36, T:0.05
Consensus pattern (18 bp):
AGGAGAAGAAGACAGCTA
Found at i:1440974 original size:21 final size:21
Alignment explanation
Indices: 1440950--1440989 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1440940 TTTTCAAAGG
1440950 CATGCACCGATGCATCAATAC
1 CATGCACCGATGCATCAATAC
*
1440971 CATGCATCGATGCATCAAT
1 CATGCACCGATGCATCAAT
1440990 GAATAAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.30, G:0.15, T:0.23
Consensus pattern (21 bp):
CATGCACCGATGCATCAATAC
Found at i:1441039 original size:19 final size:19
Alignment explanation
Indices: 1441015--1441053 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
1441005 TCGAATGCAT
1441015 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
**
1441034 TCCATGCATTGATGCACTC
1 TCCATGCACCGATGCACTC
1441053 T
1 T
1441054 AATTTAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.21, C:0.36, G:0.15, T:0.28
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:1441086 original size:64 final size:66
Alignment explanation
Indices: 1440970--1441162 Score: 202
Period size: 64 Copynumber: 3.0 Consensus size: 66
1440960 TGCATCAATA
* * * * * *
1440970 CCATGCATCGATGCATCAATG--AATAAATTGAAACATCGAATGCATTCCATGCACCGATGCACT
1 CCATGCATCGATGCA-CCATGCTATTTAATTAAAACATCGAATGCATTTCATGCATCGATGCACT
1441033 CT
65 CT
* * * *
1441035 CCATGCATTGATGCA-C-T-CTAATTTAATTAAAACATCGAATACATTTGATGCATCGATGCACA
1 CCATGCATCGATGCACCATGCT-ATTTAATTAAAACATCGAATGCATTTCATGCATCGATGCACT
*
1441097 AT
65 CT
* *
1441099 CCATGCATCGATGCACCATGCTATTT--TTCAAACATCGAATGCACTTCATGCATCGATGCACTC
1 CCATGCATCGATGCACCATGCTATTTAATTAAAACATCGAATGCATTTCATGCATCGATGCACTC
1441162 T
66 T
1441163 TAGTGCACCG
Statistics
Matches: 104, Mismatches: 18, Indels: 13
0.77 0.13 0.10
Matches are distributed among these distances:
62 1 0.01
64 81 0.78
65 15 0.14
66 5 0.05
67 2 0.02
ACGTcount: A:0.32, C:0.25, G:0.14, T:0.28
Consensus pattern (66 bp):
CCATGCATCGATGCACCATGCTATTTAATTAAAACATCGAATGCATTTCATGCATCGATGCACTC
T
Found at i:1441174 original size:19 final size:19
Alignment explanation
Indices: 1441147--1441198 Score: 95
Period size: 19 Copynumber: 2.7 Consensus size: 19
1441137 ATGCACTTCA
*
1441147 TGCATCGATGCACTCTTAG
1 TGCACCGATGCACTCTTAG
1441166 TGCACCGATGCACTCTTAG
1 TGCACCGATGCACTCTTAG
1441185 TGCACCGATGCACT
1 TGCACCGATGCACT
1441199 AGGAGTCCAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.21, C:0.31, G:0.21, T:0.27
Consensus pattern (19 bp):
TGCACCGATGCACTCTTAG
Done.