Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007746.1 Hibiscus syriacus cultivar Beakdansim tig00110009_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: 3674400
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 15
Found at i:1285356 original size:20 final size:19
Alignment explanation
Indices: 1285314--1285350 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1285304 TCCCTTTTGA
*
1285314 AGGGGAACCGATTCCCCCC
1 AGGGGAACCGATACCCCCC
*
1285333 AGGGGAATCGATACCCCC
1 AGGGGAACCGATACCCCC
1285351 TGAGGGTTCT
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:0.24, C:0.38, G:0.27, T:0.11
Consensus pattern (19 bp):
AGGGGAACCGATACCCCCC
Found at i:1291513 original size:19 final size:21
Alignment explanation
Indices: 1291489--1291530 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
1291479 CCTAAAATGA
1291489 TCTAAT-AT-AAAAATTAATT
1 TCTAATAATCAAAAATTAATT
1291508 TCTAATAATCCAAAAATTAATT
1 TCTAATAAT-CAAAAATTAATT
1291530 T
1 T
1291531 TAAACAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 6 0.30
20 2 0.10
22 12 0.60
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (21 bp):
TCTAATAATCAAAAATTAATT
Found at i:1291692 original size:21 final size:21
Alignment explanation
Indices: 1291661--1291735 Score: 68
Period size: 17 Copynumber: 3.7 Consensus size: 21
1291651 TCTGCAAAAA
*
1291661 AAATTAATTAAATACAATATT
1 AAATAAATTAAATACAATATT
*
1291682 AAATAATTTAAATAC----TT
1 AAATAAATTAAATACAATATT
*
1291699 AAATAAATTAAATAAAAATATT
1 AAATAAATTAAAT-ACAATATT
*
1291721 AAATATAATAAAATA
1 AAATA-AATTAAATA
1291736 TACTTTAAAC
Statistics
Matches: 43, Mismatches: 5, Indels: 11
0.73 0.08 0.19
Matches are distributed among these distances:
17 14 0.33
18 1 0.02
21 13 0.30
22 8 0.19
23 7 0.16
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.35
Consensus pattern (21 bp):
AAATAAATTAAATACAATATT
Found at i:1291725 original size:22 final size:24
Alignment explanation
Indices: 1291691--1291735 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
1291681 TAAATAATTT
*
1291691 AAATACTTAAATA-AATTAAATAA
1 AAATACTTAAATATAATAAAATAA
1291714 AAATA-TTAAATATAATAAAATA
1 AAATACTTAAATATAATAAAATA
1291736 TACTTTAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (24 bp):
AAATACTTAAATATAATAAAATAA
Found at i:1292909 original size:48 final size:48
Alignment explanation
Indices: 1292833--1292929 Score: 176
Period size: 48 Copynumber: 2.0 Consensus size: 48
1292823 TTAGGGACCT
*
1292833 TATTAATATTTTCTGAAAGTACAGAACCTATTCGTAAATAATCTTAAG
1 TATTAATATTTTCTGAAAGTACAAAACCTATTCGTAAATAATCTTAAG
*
1292881 TATTAATATTTTCTGAAAGTACAAAACCTATTCGTAAATAATTTTAAG
1 TATTAATATTTTCTGAAAGTACAAAACCTATTCGTAAATAATCTTAAG
1292929 T
1 T
1292930 TAACCAAATT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.40, C:0.11, G:0.09, T:0.39
Consensus pattern (48 bp):
TATTAATATTTTCTGAAAGTACAAAACCTATTCGTAAATAATCTTAAG
Found at i:1298316 original size:13 final size:13
Alignment explanation
Indices: 1298298--1298341 Score: 70
Period size: 13 Copynumber: 3.4 Consensus size: 13
1298288 GCAATGCGCA
1298298 TCATAAATACGCG
1 TCATAAATACGCG
*
1298311 TCATAAATACGTG
1 TCATAAATACGCG
*
1298324 TCATAAATGCGCG
1 TCATAAATACGCG
1298337 TCATA
1 TCATA
1298342 GATTTATGAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.27
Consensus pattern (13 bp):
TCATAAATACGCG
Found at i:1304818 original size:17 final size:18
Alignment explanation
Indices: 1304796--1304829 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1304786 CATTAAGTTA
1304796 AAATTAAT-ATTTTAAAT
1 AAATTAATAATTTTAAAT
*
1304813 AAATTATTAATTTTAAA
1 AAATTAATAATTTTAAA
1304830 ATTGAATTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
AAATTAATAATTTTAAAT
Found at i:1306957 original size:55 final size:55
Alignment explanation
Indices: 1306873--1307226 Score: 577
Period size: 55 Copynumber: 6.4 Consensus size: 55
1306863 AAATTTATAT
* * *
1306873 ACTTAATATGAATTTCCT-AGTTTTGCACATAAAGTGCCCATACAGAAATTCATCC
1 ACTTAGTATGAATTTCTTAAG-TTTACACATAAAGTGCCCATACAGAAATTCATCC
* *
1306928 ACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATACGGAAATTTATCC
1 ACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATACAGAAATTCATCC
* *
1306983 ACTTAGTATGAATTTCTTAAGTTTACATATAAAGTGCCCATACAGAAATTCATCT
1 ACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATACAGAAATTCATCC
*
1307038 ACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGTCCATACAGAAATTCATCC
1 ACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATACAGAAATTCATCC
*
1307093 ACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATAC-GAAAATTCTTCC
1 ACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATACAG-AAATTCATCC
* *
1307148 ACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGGCCATACAAAAATTCATCC
1 ACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATACAGAAATTCATCC
1307203 ACTTAGTATGAATTTCTTAAGTTT
1 ACTTAGTATGAATTTCTTAAGTTT
1307227 TTACACACTT
Statistics
Matches: 279, Mismatches: 17, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
54 1 0.00
55 276 0.99
56 2 0.01
ACGTcount: A:0.35, C:0.18, G:0.11, T:0.35
Consensus pattern (55 bp):
ACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATACAGAAATTCATCC
Found at i:1314864 original size:55 final size:55
Alignment explanation
Indices: 1314791--1315093 Score: 366
Period size: 55 Copynumber: 5.7 Consensus size: 55
1314781 CCCACTACCA
* * *
1314791 ATACGAAAATT-ATACACTTAGTATGAATTTCCT-AGTTTTACACATAAAGTACCC
1 ATACGAAAATTCATCCACTTAGTATGAATTTCTTAAG-TTTACACATAAAGTGCCC
* *
1314845 AAACCG-AAATTCATCCACTTAGTATGAATTTCTTAAGTTTACTCATAAAGTGCCC
1 ATA-CGAAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCC
* * *
1314900 ATACGAAAATTCATCAACATAGTATGAATTTCTTAAGTTTACACATAAAGTTCCC
1 ATACGAAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCC
*
1314955 ATACGGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCC
1 ATACGAAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCC
*
1315010 ATACGAAAACTCATCCAC----------TTT-TTAAGTTTACACATAAAGTGCCC
1 ATACGAAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCC
* *
1315054 ATAC-AGAAATTCGTCGACTTAGTATGAATTTCTTAAGTTT
1 ATACGA-AAATTCATCCACTTAGTATGAATTTCTTAAGTTT
1315094 TTGCACACTT
Statistics
Matches: 214, Mismatches: 19, Indels: 31
0.81 0.07 0.12
Matches are distributed among these distances:
43 1 0.00
44 36 0.17
45 3 0.01
54 12 0.06
55 160 0.75
56 2 0.01
ACGTcount: A:0.36, C:0.19, G:0.11, T:0.33
Consensus pattern (55 bp):
ATACGAAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCC
Found at i:1315573 original size:20 final size:19
Alignment explanation
Indices: 1315523--1315574 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 19
1315513 TTGTTTGAAT
*
1315523 GGTATCGATAACTTCCCTTC
1 GGTATCGAT-ACTCCCCTTC
*
1315543 AGTATCGATACTCCCCTTTC
1 GGTATCGATACTCCCC-TTC
1315563 GGTATCGATACT
1 GGTATCGATACT
1315575 GATTGCATCA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 6 0.21
20 22 0.79
ACGTcount: A:0.21, C:0.29, G:0.15, T:0.35
Consensus pattern (19 bp):
GGTATCGATACTCCCCTTC
Found at i:1317233 original size:275 final size:275
Alignment explanation
Indices: 1316742--1317303 Score: 1070
Period size: 275 Copynumber: 2.0 Consensus size: 275
1316732 CGATATTCAT
*
1316742 TGAATTGTATATTCGTTTAGATATCGATCGAAGACAAGTCCAAGATGGTTTGAAGTTATAAGAGT
1 TGAATTGTATATTCGTGTAGATATCGATCGAAGACAAGTCCAAGATGGTTTGAAGTTATAAGAGT
*
1316807 GTATAAGAGTTGTACGTATATGAATGGCTAGTGAGGTCTAGGTGAGTGCATACTAGTTGATATAT
66 GTATAAGAGTTGTACGTATAGGAATGGCTAGTGAGGTCTAGGTGAGTGCATACTAGTTGATATAT
*
1316872 GATGTTTAATGGAAATAATACTTGCGATGAGTCTATTTCCTATATTATAATGCATGAATTCATGA
131 GATGTTTAATGGAAATAATACTTGCGATGAGTCTATTTCCTATATTATAATGCAGGAATTCATGA
1316937 ATGTAGGCATGTGTTTGATATGAGTATATGTGTTATATGTTACATGATCCATGGGAATATATGTT
196 ATGTAGGCATGTGTTTGATATGAGTATATGTGTTATATGTTACATGATCCATGGGAATATATGTT
1317002 GTCTGATAAACCATG
261 GTCTGATAAACCATG
*
1317017 TGAATTGTATATTCGTGTAGATATCGATCGAATACAAGTCCAAGATGGTTTGAAGTTATAAGAGT
1 TGAATTGTATATTCGTGTAGATATCGATCGAAGACAAGTCCAAGATGGTTTGAAGTTATAAGAGT
1317082 GTATAAGAGTTGTACGTATAGGAATGGCTAGTGAGGTCTAGGTGAGTGCATACTAGTTGATATAT
66 GTATAAGAGTTGTACGTATAGGAATGGCTAGTGAGGTCTAGGTGAGTGCATACTAGTTGATATAT
1317147 GATGTTTAATGGAAATAATACTTGCGATGAGTCTATTTCCTATATTATAATGCAGGAATTCATGA
131 GATGTTTAATGGAAATAATACTTGCGATGAGTCTATTTCCTATATTATAATGCAGGAATTCATGA
1317212 ATGTAGGCATGTGTTTGATATGAGTATATGTGTTATATGTTACATGATCCATGGGAATATATGTT
196 ATGTAGGCATGTGTTTGATATGAGTATATGTGTTATATGTTACATGATCCATGGGAATATATGTT
*
1317277 GTTTGATAAACCATG
261 GTCTGATAAACCATG
1317292 TGAATTGATATA
1 TGAATTG-TATA
1317304 AATGATATAT
Statistics
Matches: 281, Mismatches: 5, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
275 277 0.99
276 4 0.01
ACGTcount: A:0.31, C:0.09, G:0.23, T:0.36
Consensus pattern (275 bp):
TGAATTGTATATTCGTGTAGATATCGATCGAAGACAAGTCCAAGATGGTTTGAAGTTATAAGAGT
GTATAAGAGTTGTACGTATAGGAATGGCTAGTGAGGTCTAGGTGAGTGCATACTAGTTGATATAT
GATGTTTAATGGAAATAATACTTGCGATGAGTCTATTTCCTATATTATAATGCAGGAATTCATGA
ATGTAGGCATGTGTTTGATATGAGTATATGTGTTATATGTTACATGATCCATGGGAATATATGTT
GTCTGATAAACCATG
Found at i:1317664 original size:22 final size:22
Alignment explanation
Indices: 1317636--1317677 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1317626 AATCGAGGGT
*
1317636 TACATAGGTCCTTCAGGACATA
1 TACATAGGTCATTCAGGACATA
*
1317658 TACATAGGTCATTCGGGACA
1 TACATAGGTCATTCAGGACA
1317678 AATTTCATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.26
Consensus pattern (22 bp):
TACATAGGTCATTCAGGACATA
Found at i:1317944 original size:18 final size:18
Alignment explanation
Indices: 1317913--1317958 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
1317903 AGCATATGAC
* *
1317913 TAAGAGATATGAATGATAA
1 TAAG-GATAAGAATAATAA
*
1317932 TAATGATAAGAATAATAA
1 TAAGGATAAGAATAATAA
1317950 TAAGGATAA
1 TAAGGATAA
1317959 TGAGGTTATA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
18 20 0.87
19 3 0.13
ACGTcount: A:0.57, C:0.00, G:0.17, T:0.26
Consensus pattern (18 bp):
TAAGGATAAGAATAATAA
Found at i:1321287 original size:31 final size:31
Alignment explanation
Indices: 1321249--1321322 Score: 148
Period size: 31 Copynumber: 2.4 Consensus size: 31
1321239 AATTAAAGAA
1321249 GGAATTAAAGAATCAACCATTCATCCAAAAT
1 GGAATTAAAGAATCAACCATTCATCCAAAAT
1321280 GGAATTAAAGAATCAACCATTCATCCAAAAT
1 GGAATTAAAGAATCAACCATTCATCCAAAAT
1321311 GGAATTAAAGAA
1 GGAATTAAAGAA
1321323 GGAATTAACA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.50, C:0.16, G:0.12, T:0.22
Consensus pattern (31 bp):
GGAATTAAAGAATCAACCATTCATCCAAAAT
Found at i:1331601 original size:54 final size:53
Alignment explanation
Indices: 1331538--1332100 Score: 777
Period size: 54 Copynumber: 10.5 Consensus size: 53
1331528 ATAAGTTCTC
* * *
1331538 TGGGGTGCACACGTAGTGCCAATACGGTTGTTCATCAACATATGATGAATTATG
1 TGGGTTGCACACTTAGTGCCTATACGGTTGTTCATCAACATATGATGAATT-TG
* * ** **
1331592 TTGGTTGCACACTTAGTGCATATATAGTCATTCATCAACATATGATGAATTTCG
1 TGGGTTGCACACTTAGTGCCTATACGGTTGTTCATCAACATATGATGAATTT-G
* * * *
1331646 TCGGTTGCACACTTAGTGCCTATAAGGTTATTCATCAACATATGATGAATTCTT
1 TGGGTTGCACACTTAGTGCCTATACGGTTGTTCATCAACATATGATGAATT-TG
* *
1331700 TGGGTTGCACACTTAGTGCCTATACGGTTGTCCATCAACATATGATGAATTCTT
1 TGGGTTGCACACTTAGTGCCTATACGGTTGTTCATCAACATATGATGAATT-TG
1331754 TGGGTTGCACACTTAGTGCCTATACGGTTGTTCATCAACATATGATGAATTCTG
1 TGGGTTGCACACTTAGTGCCTATACGGTTGTTCATCAACATATGATGAATT-TG
* **
1331808 TGGGTTGCACACTTAGTGCCTATACAGTCATTCATCAACATATGATGAATTTCG
1 TGGGTTGCACACTTAGTGCCTATACGGTTGTTCATCAACATATGATGAATTT-G
1331862 TGGGTTGCACACTTAGTGCCTATACGGTTGTTCATCAACATATGATGAATTT-
1 TGGGTTGCACACTTAGTGCCTATACGGTTGTTCATCAACATATGATGAATTTG
* * * * **
1331914 TGTTGTTGCACACATAGTGCTTATAAGGTTGTTCATCAACATATGATGAATTACA
1 TG-GGTTGCACACTTAGTGCCTATACGGTTGTTCATCAACATATGATGAATT-TG
* *
1331969 TGGGTTGCACAATTAGTGCCTATATGGTTGTTCATCAACATATGATGAATTTCG
1 TGGGTTGCACACTTAGTGCCTATACGGTTGTTCATCAACATATGATGAATTT-G
* *
1332023 TGGGTTGCACACTTAGTGCCTATACGGTTGTTCATAAATATATGATGAATTTCG
1 TGGGTTGCACACTTAGTGCCTATACGGTTGTTCATCAACATATGATGAATTT-G
1332077 TGGGTTGCACACTTAGTGCCTATA
1 TGGGTTGCACACTTAGTGCCTATA
1332101 GTACACATAG
Statistics
Matches: 459, Mismatches: 43, Indels: 14
0.89 0.08 0.03
Matches are distributed among these distances:
52 2 0.00
53 47 0.10
54 407 0.89
55 3 0.01
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (53 bp):
TGGGTTGCACACTTAGTGCCTATACGGTTGTTCATCAACATATGATGAATTTG
Found at i:1337128 original size:54 final size:54
Alignment explanation
Indices: 1337044--1337310 Score: 401
Period size: 54 Copynumber: 4.9 Consensus size: 54
1337034 GTCGATACAA
* * *
1337044 TTGTTCATTAACATATGATGAATTCAGTGGGTTGCACACTTAGTGCATATACGG
1 TTGTTCATCAACATATGATGAATTCTGTGGGTTGCACACTTAGTGCTTATACGG
**
1337098 TCATTCATCAACATATGATGAATTCTGTGGGTTGCACACTTAGTGCTTATACGG
1 TTGTTCATCAACATATGATGAATTCTGTGGGTTGCACACTTAGTGCTTATACGG
* * * ** *
1337152 TTGTTCATCAACATATGATGAATTTTGTGGGTTGCAAACTTAGTCCCGATACTG
1 TTGTTCATCAACATATGATGAATTCTGTGGGTTGCACACTTAGTGCTTATACGG
*
1337206 TTGTTCATCAACATATGATGAATTTTGTGGGTTGCACACTTAGTG-TCTATACGG
1 TTGTTCATCAACATATGATGAATTCTGTGGGTTGCACACTTAGTGCT-TATACGG
*
1337260 TTGTTCATCAACATATGATGAATTCCGTGGGTTGCACACTTAGTGCTTATA
1 TTGTTCATCAACATATGATGAATTCTGTGGGTTGCACACTTAGTGCTTATA
1337311 GTATACACAA
Statistics
Matches: 191, Mismatches: 20, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
54 190 0.99
55 1 0.01
ACGTcount: A:0.26, C:0.16, G:0.21, T:0.37
Consensus pattern (54 bp):
TTGTTCATCAACATATGATGAATTCTGTGGGTTGCACACTTAGTGCTTATACGG
Found at i:1342567 original size:21 final size:20
Alignment explanation
Indices: 1342539--1342577 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
1342529 CATTGCAGGA
*
1342539 ATTTATGGCCTCGACAAAAG
1 ATTTATGGCCTCAACAAAAG
*
1342559 ATTTCATGGCTTCAACAAA
1 ATTT-ATGGCCTCAACAAA
1342578 GATCTTGATA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.28
Consensus pattern (20 bp):
ATTTATGGCCTCAACAAAAG
Found at i:1343535 original size:24 final size:24
Alignment explanation
Indices: 1343506--1343581 Score: 72
Period size: 24 Copynumber: 3.3 Consensus size: 24
1343496 TTACCATTTA
1343506 TTTACCATAAGCTCGTAAGCTTAT
1 TTTACCATAAGCTCGTAAGCTTAT
* * *
1343530 TTTACCA-AA-ATAC-TTA-C-CAT
1 TTTACCATAAGCT-CGTAAGCTTAT
1343550 TTGTACCATAAGCTCGTAAGCTTAT
1 TT-TACCATAAGCTCGTAAGCTTAT
1343575 TTTACCA
1 TTTACCA
1343582 ATACACTTGC
Statistics
Matches: 39, Mismatches: 6, Indels: 14
0.66 0.10 0.24
Matches are distributed among these distances:
20 4 0.10
21 6 0.15
22 6 0.15
23 6 0.15
24 13 0.33
25 4 0.10
ACGTcount: A:0.32, C:0.22, G:0.09, T:0.37
Consensus pattern (24 bp):
TTTACCATAAGCTCGTAAGCTTAT
Found at i:1343595 original size:45 final size:45
Alignment explanation
Indices: 1343508--1343595 Score: 149
Period size: 45 Copynumber: 2.0 Consensus size: 45
1343498 ACCATTTATT
*
1343508 TACCATAAGCTCGTAAGCTTATTTTACCAAAATACTTACCATTTG
1 TACCATAAGCTCGTAAGCTTATTTTACCAAAACACTTACCATTTG
* *
1343553 TACCATAAGCTCGTAAGCTTATTTTACCAATACACTTGCCATT
1 TACCATAAGCTCGTAAGCTTATTTTACCAAAACACTTACCATT
1343596 ATTCCATAAC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.32, C:0.24, G:0.09, T:0.35
Consensus pattern (45 bp):
TACCATAAGCTCGTAAGCTTATTTTACCAAAACACTTACCATTTG
Found at i:1362983 original size:6 final size:6
Alignment explanation
Indices: 1362974--1363016 Score: 59
Period size: 6 Copynumber: 7.2 Consensus size: 6
1362964 CAGGAAAAAG
* * *
1362974 AAATAA AAATAA AAATAA AAATAA AGATGA CAATAA AAATAA A
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA A
1363017 TTCATTATTT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.77, C:0.02, G:0.05, T:0.16
Consensus pattern (6 bp):
AAATAA
Found at i:1365167 original size:18 final size:19
Alignment explanation
Indices: 1365144--1365186 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
1365134 GAAAATATTC
*
1365144 TTTTTATTTTA-TTCCTTT
1 TTTTTATTTTATTTCCTTA
1365162 TTTTTATTTTATTTCCTTA
1 TTTTTATTTTATTTCCTTA
1365181 TTTTTA
1 TTTTTA
1365187 CTTCTCACTC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 11 0.48
19 12 0.52
ACGTcount: A:0.14, C:0.09, G:0.00, T:0.77
Consensus pattern (19 bp):
TTTTTATTTTATTTCCTTA
Found at i:1370738 original size:12 final size:12
Alignment explanation
Indices: 1370706--1370745 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
1370696 TCAAATAACA
1370706 TTAAAA-TTA-T
1 TTAAAATTTATT
*
1370716 TT-AAATCTATT
1 TTAAAATTTATT
1370727 TTAAAATTTATT
1 TTAAAATTTATT
1370739 TTAAAAT
1 TTAAAAT
1370746 ATGGATTGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
9 3 0.12
10 4 0.16
11 3 0.12
12 15 0.60
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (12 bp):
TTAAAATTTATT
Found at i:1370757 original size:22 final size:22
Alignment explanation
Indices: 1370732--1371186 Score: 651
Period size: 22 Copynumber: 20.6 Consensus size: 22
1370722 CTATTTTAAA
1370732 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
*
1370754 ATTTTTTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
*
1370776 ATTTATTTTAAAATATAGATTG
1 ATTTATTTTAAAATATGGATTG
*
1370798 ATTTATTTTAAAATATAGATTG
1 ATTTATTTTAAAATATGGATTG
*
1370820 ATTTATTTTAAAATATGGATTA
1 ATTTATTTTAAAATATGGATTG
*
1370842 ATTTATTTTAAAATATGAATTG
1 ATTTATTTTAAAATATGGATTG
***
1370864 ATTTATTTTAAAATATGGAAAA
1 ATTTATTTTAAAATATGGATTG
1370886 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
1370908 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
**
1370930 ATTTATTTTAAAATATGGA-AA
1 ATTTATTTTAAAATATGGATTG
* *
1370951 ATTTTATTTTTAAATTTGGATTG
1 A-TTTATTTTAAAATATGGATTG
* *
1370974 ATTTATTTTAAAATATTGATGG
1 ATTTATTTTAAAATATGGATTG
*
1370996 AATTATTTTTAAAATATGGATTG
1 ATTTA-TTTTAAAATATGGATTG
***
1371019 ATTTATTTTAAAATATGGAAAA
1 ATTTATTTTAAAATATGGATTG
* * *
1371041 ATTTATTTTTAAATTTGAATTG
1 ATTTATTTTAAAATATGGATTG
* *
1371063 ATTTATTTTAAAATGTTGATTG
1 ATTTATTTTAAAATATGGATTG
*
1371085 ATTTATTTTAAAATATGGATTA
1 ATTTATTTTAAAATATGGATTG
1371107 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
1371129 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
*
1371151 ATTTATTTTAAAATTTGGATTG
1 ATTTATTTTAAAATATGGATTG
1371173 ATTTATTTTTAAAA
1 ATTTA-TTTTAAAA
1371187 AAAATTATTA
Statistics
Matches: 383, Mismatches: 46, Indels: 7
0.88 0.11 0.02
Matches are distributed among these distances:
21 1 0.00
22 354 0.92
23 28 0.07
ACGTcount: A:0.38, C:0.00, G:0.11, T:0.51
Consensus pattern (22 bp):
ATTTATTTTAAAATATGGATTG
Found at i:1371268 original size:31 final size:31
Alignment explanation
Indices: 1371211--1371269 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
1371201 AGTTGTATGG
*
1371211 ATTATTTAAATTTCAGTATTATAAAACTAAA
1 ATTATTTAAATTTCAGTATTACAAAACTAAA
* * *
1371242 ATTATTTCAATTTTAGTATTGCAAAACT
1 ATTATTTAAATTTCAGTATTACAAAACT
1371270 CTTTTAAGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.42, C:0.08, G:0.05, T:0.44
Consensus pattern (31 bp):
ATTATTTAAATTTCAGTATTACAAAACTAAA
Found at i:1376375 original size:17 final size:17
Alignment explanation
Indices: 1376353--1376392 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
1376343 ACTATGGTAC
1376353 CGATACTCCCTTAGTAT
1 CGATACTCCCTTAGTAT
1376370 CGATACTCCCTTAGTAT
1 CGATACTCCCTTAGTAT
*
1376387 TGATAC
1 CGATAC
1376393 CATTTCTACA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.25, C:0.28, G:0.12, T:0.35
Consensus pattern (17 bp):
CGATACTCCCTTAGTAT
Found at i:1391462 original size:6 final size:6
Alignment explanation
Indices: 1391451--1391596 Score: 260
Period size: 6 Copynumber: 24.7 Consensus size: 6
1391441 TCTTTTCCTA
*
1391451 CTTCTC CTTCTC ATTCTC CTTCTC C-T-TC CTTCTC CTTCTC CTTCTC
1 CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC
1391497 CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC
1 CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC
*
1391545 CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC CTTCTT
1 CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC
1391593 CTTC
1 CTTC
1391597 ACATTTATCA
Statistics
Matches: 135, Mismatches: 3, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
4 3 0.02
5 2 0.01
6 130 0.96
ACGTcount: A:0.01, C:0.49, G:0.00, T:0.51
Consensus pattern (6 bp):
CTTCTC
Found at i:1392482 original size:21 final size:21
Alignment explanation
Indices: 1392440--1392482 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
1392430 ATGATATATT
* *
1392440 AAATTATATTTTTTAACTATA
1 AAATTATATCTTTTAACAATA
1392461 AAATTAATATCTTTTAA-AATA
1 AAATT-ATATCTTTTAACAATA
1392482 A
1 A
1392483 TTTTATCTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.47
Consensus pattern (21 bp):
AAATTATATCTTTTAACAATA
Found at i:1392950 original size:34 final size:34
Alignment explanation
Indices: 1392912--1392978 Score: 116
Period size: 34 Copynumber: 2.0 Consensus size: 34
1392902 TTTAATTTAA
1392912 GGTTTAGAATATAATTGAAGTATTTTGGAATTTG
1 GGTTTAGAATATAATTGAAGTATTTTGGAATTTG
* *
1392946 GGTTTAGAATGTAATTGAAGTGTTTTGGAATTT
1 GGTTTAGAATATAATTGAAGTATTTTGGAATTT
1392979 TGAACATGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.30, C:0.00, G:0.25, T:0.45
Consensus pattern (34 bp):
GGTTTAGAATATAATTGAAGTATTTTGGAATTTG
Found at i:1408020 original size:60 final size:60
Alignment explanation
Indices: 1407907--1408021 Score: 144
Period size: 60 Copynumber: 1.9 Consensus size: 60
1407897 AGTATGATTA
* * *
1407907 TCATTCTAAATTAGTCCTCAAACTTTTGAATATTTCAATTTCATCCTTAAACTATGGCAT
1 TCATTCTAAATTAGTCCTCAAACTTTTGAACATTCCAATTTCATCCTCAAACTATGGCAT
* * *
1407967 TCATTCTAAATTAATTCCT-AAACTTTTTAAGCATTCCAATTTCATCC-CGAACTAT
1 TCATTCTAAATT-AGTCCTCAAACTTTTGAA-CATTCCAATTTCATCCTCAAACTAT
1408022 ACACATATAC
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
60 28 0.60
61 19 0.40
ACGTcount: A:0.32, C:0.22, G:0.05, T:0.41
Consensus pattern (60 bp):
TCATTCTAAATTAGTCCTCAAACTTTTGAACATTCCAATTTCATCCTCAAACTATGGCAT
Found at i:1408247 original size:60 final size:60
Alignment explanation
Indices: 1408154--1408276 Score: 151
Period size: 60 Copynumber: 2.0 Consensus size: 60
1408144 TGAATTTGGA
** *
1408154 GATGAAATTGAAATATTCAAAAGTTTGGGGACCAATTTAGAAA-G-AGAGTCATAGTTTAGG
1 GATGAAATTGAAATATTCAAAAGTTTAAGGACCAATCTA-AAATGAAG-GTCATAGTTTAGG
* * * *
1408214 GATGAAATTGACATCTTTAAAAGTTTAAGGACCAATCTAAAATGAAGGTTATAGTTTAGG
1 GATGAAATTGAAATATTCAAAAGTTTAAGGACCAATCTAAAATGAAGGTCATAGTTTAGG
1408274 GAT
1 GAT
1408277 ATATGATGCA
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
59 3 0.06
60 49 0.91
61 2 0.04
ACGTcount: A:0.40, C:0.07, G:0.23, T:0.30
Consensus pattern (60 bp):
GATGAAATTGAAATATTCAAAAGTTTAAGGACCAATCTAAAATGAAGGTCATAGTTTAGG
Found at i:1410387 original size:13 final size:13
Alignment explanation
Indices: 1410369--1410395 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1410359 TGTCTTGTAG
1410369 TAGTTTATAGCCT
1 TAGTTTATAGCCT
1410382 TAGTTTATAGCCT
1 TAGTTTATAGCCT
1410395 T
1 T
1410396 CAACCATGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.15, G:0.15, T:0.48
Consensus pattern (13 bp):
TAGTTTATAGCCT
Found at i:1415516 original size:21 final size:21
Alignment explanation
Indices: 1415463--1415508 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
1415453 CTTAAACCCC
* * * *
1415463 TAAACCATAGACTATAAATCA
1 TAAACCCTAAACTCTAAATAA
1415484 TAAACCCTAAACTCTAAATAA
1 TAAACCCTAAACTCTAAATAA
1415505 TAAA
1 TAAA
1415509 TCTTAAACAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.54, C:0.20, G:0.02, T:0.24
Consensus pattern (21 bp):
TAAACCCTAAACTCTAAATAA
Found at i:1415528 original size:28 final size:28
Alignment explanation
Indices: 1415476--1415529 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
1415466 ACCATAGACT
* *
1415476 ATAAATCATAAACCCTAAACTCTAAATA
1 ATAAATCATAAACACTAAACCCTAAATA
* *
1415504 ATAAATCTTAAACACTATACCCTAAA
1 ATAAATCATAAACACTAAACCCTAAA
1415530 ACCATAATAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.52, C:0.22, G:0.00, T:0.26
Consensus pattern (28 bp):
ATAAATCATAAACACTAAACCCTAAATA
Found at i:1415572 original size:14 final size:13
Alignment explanation
Indices: 1415555--1415613 Score: 55
Period size: 14 Copynumber: 4.2 Consensus size: 13
1415545 CCATGGTTCA
1415555 TAAACATTGAACCT
1 TAAACATT-AACCT
*
1415569 TAAACACTAAACCCT
1 TAAACA-TTAA-CCT
1415584 TAAACACTTAACCT
1 TAAACA-TTAACCT
*
1415598 TAAATCATAAACCT
1 TAAA-CATTAACCT
1415612 TA
1 TA
1415614 CACCTTACAT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
14 23 0.59
15 16 0.41
ACGTcount: A:0.46, C:0.25, G:0.02, T:0.27
Consensus pattern (13 bp):
TAAACATTAACCT
Found at i:1415586 original size:15 final size:15
Alignment explanation
Indices: 1415566--1415610 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
1415556 AAACATTGAA
1415566 CCTTAAACACTAAAC
1 CCTTAAACACTAAAC
*
1415581 CCTTAAACACTTAA-
1 CCTTAAACACTAAAC
1415595 CCTTAAATCA-TAAAC
1 CCTTAAA-CACTAAAC
1415610 C
1 C
1415611 TTACACCTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
14 10 0.38
15 16 0.62
ACGTcount: A:0.44, C:0.31, G:0.00, T:0.24
Consensus pattern (15 bp):
CCTTAAACACTAAAC
Found at i:1415588 original size:29 final size:29
Alignment explanation
Indices: 1415555--1415645 Score: 84
Period size: 29 Copynumber: 3.2 Consensus size: 29
1415545 CCATGGTTCA
1415555 TAAACA-TTGAACCTTAAA-CACTAAACCCT
1 TAAACACTT-AACCTTAAATCA-TAAACCCT
1415584 TAAACACTTAACCTTAAATCATAAA-CCT
1 TAAACACTTAACCTTAAATCATAAACCCT
* *
1415612 TACAC-CTT-ACATAATAAATCATAAACCCT
1 TAAACACTTAACCT--TAAATCATAAACCCT
*
1415641 AAAAC
1 TAAAC
1415646 CTAAACTATA
Statistics
Matches: 53, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
26 3 0.06
27 3 0.06
28 18 0.34
29 25 0.47
30 4 0.08
ACGTcount: A:0.47, C:0.26, G:0.01, T:0.25
Consensus pattern (29 bp):
TAAACACTTAACCTTAAATCATAAACCCT
Found at i:1415609 original size:21 final size:21
Alignment explanation
Indices: 1415584--1415629 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
1415574 ACTAAACCCT
*
1415584 TAAACACTTA-ACCTTAAATCA
1 TAAAC-CTTACACCTTAAATAA
*
1415605 TAAACCTTACACCTTACATAA
1 TAAACCTTACACCTTAAATAA
1415626 TAAA
1 TAAA
1415630 TCATAAACCC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 4 0.18
21 18 0.82
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.28
Consensus pattern (21 bp):
TAAACCTTACACCTTAAATAA
Found at i:1415825 original size:14 final size:14
Alignment explanation
Indices: 1415809--1415913 Score: 83
Period size: 15 Copynumber: 7.4 Consensus size: 14
1415799 ATTAATCCAT
1415809 AAACTATAAACCTTA
1 AAACTATAAACC-TA
*
1415824 AAACTCTAAACTCTA
1 AAACTATAAAC-CTA
1415839 AAACTATAAAGCCTA
1 AAACTATAAA-CCTA
1415854 AAAC-ATAAACC-A
1 AAACTATAAACCTA
* *
1415866 TAGACTTTAAAGCCTA
1 -AAACTATAAA-CCTA
1415882 AAAC-ATAAACCCT-
1 AAACTATAAA-CCTA
**
1415895 AAACCCTAAACCTA
1 AAACTATAAACCTA
1415909 AAACT
1 AAACT
1415914 CTAGGCCCTA
Statistics
Matches: 73, Mismatches: 9, Indels: 17
0.74 0.09 0.17
Matches are distributed among these distances:
12 1 0.01
13 12 0.16
14 24 0.33
15 33 0.45
16 3 0.04
ACGTcount: A:0.51, C:0.25, G:0.03, T:0.21
Consensus pattern (14 bp):
AAACTATAAACCTA
Found at i:1415883 original size:21 final size:21
Alignment explanation
Indices: 1415815--1416010 Score: 63
Period size: 21 Copynumber: 9.1 Consensus size: 21
1415805 CCATAAACTA
* * *
1415815 TAAACCTTAAAACTCTAAACTC
1 TAAACCAT-AAACCCTAAACCC
* * * *
1415837 TAAAACTATAAAGCCTAAAACA
1 T-AAACCATAAACCCTAAACCC
* ** *
1415859 TAAACCATAGACTTTAAAGCC
1 TAAACCATAAACCCTAAACCC
*
1415880 TAAAACATAAACCCTAAACCC
1 TAAACCATAAACCCTAAACCC
* **
1415901 TAAACC-TAAAACTCTAGGCCC
1 TAAACCAT-AAACCCTAAACCC
* * * **
1415922 TAAAACAACAAACACTAAAATC
1 T-AAACCATAAACCCTAAACCC
* *
1415944 TAAATCCAAAAATCCTAAACCC
1 TAAA-CCATAAACCCTAAACCC
* * * *
1415966 TATA-CACTAAAACTTAAACCT
1 TAAACCA-TAAACCCTAAACCC
* *
1415987 TAAAACATTAAACCATAAACCC
1 TAAACCA-TAAACCCTAAACCC
1416009 TA
1 TA
1416011 GATATTAAAA
Statistics
Matches: 121, Mismatches: 46, Indels: 14
0.67 0.25 0.08
Matches are distributed among these distances:
20 3 0.02
21 61 0.50
22 52 0.43
23 5 0.04
ACGTcount: A:0.51, C:0.27, G:0.03, T:0.20
Consensus pattern (21 bp):
TAAACCATAAACCCTAAACCC
Found at i:1415904 original size:28 final size:28
Alignment explanation
Indices: 1415845--1415912 Score: 93
Period size: 28 Copynumber: 2.5 Consensus size: 28
1415835 TCTAAAACTA
* **
1415845 TAAAGCCTAAAACATAAACCATAGACTT
1 TAAAGCCTAAAACATAAACCATAAACCC
*
1415873 TAAAGCCTAAAACATAAACCCTAAACCC
1 TAAAGCCTAAAACATAAACCATAAACCC
1415901 TAAA-CCTAAAAC
1 TAAAGCCTAAAAC
1415913 TCTAGGCCCT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
27 8 0.22
28 28 0.78
ACGTcount: A:0.51, C:0.26, G:0.04, T:0.18
Consensus pattern (28 bp):
TAAAGCCTAAAACATAAACCATAAACCC
Found at i:1415990 original size:14 final size:14
Alignment explanation
Indices: 1415973--1416062 Score: 56
Period size: 15 Copynumber: 6.3 Consensus size: 14
1415963 CCCTATACAC
1415973 TAAAACTTAAACCT
1 TAAAACTTAAACCT
*
1415987 TAAAACATTAAACCA
1 TAAAAC-TTAAACCT
* * * **
1416002 TAAACCCTAGATAT
1 TAAAACTTAAACCT
*
1416016 TAAAACCTAAA-CT
1 TAAAACTTAAACCT
* *
1416029 TTAAACTTTAAACCC
1 TAAAAC-TTAAACCT
*
1416044 TAAATCTTAAAACCT
1 TAAAACTT-AAACCT
1416059 TAAA
1 TAAA
1416063 CATAAACTCT
Statistics
Matches: 56, Mismatches: 16, Indels: 7
0.71 0.20 0.09
Matches are distributed among these distances:
13 6 0.11
14 24 0.43
15 26 0.46
ACGTcount: A:0.50, C:0.21, G:0.01, T:0.28
Consensus pattern (14 bp):
TAAAACTTAAACCT
Found at i:1416041 original size:35 final size:35
Alignment explanation
Indices: 1415981--1416088 Score: 121
Period size: 35 Copynumber: 3.0 Consensus size: 35
1415971 ACTAAAACTT
*
1415981 AAACCTTAAAACATTAAAC-CATAAACCCTAGATATTA
1 AAACCTT-AAACA-TAAACTC-TAAACCCTAAATATTA
* * *
1416018 AAACC-TAAACTTTAAACTTTAAACCCTAAATCTTA
1 AAACCTTAAAC-ATAAACTCTAAACCCTAAATATTA
*
1416053 AAACCTTAAACATAAACTCTAAACCCTAAATCTTA
1 AAACCTTAAACATAAACTCTAAACCCTAAATATTA
1416088 A
1 A
1416089 TCCATATACA
Statistics
Matches: 62, Mismatches: 6, Indels: 8
0.82 0.08 0.11
Matches are distributed among these distances:
35 51 0.82
36 6 0.10
37 5 0.08
ACGTcount: A:0.49, C:0.23, G:0.01, T:0.27
Consensus pattern (35 bp):
AAACCTTAAACATAAACTCTAAACCCTAAATATTA
Found at i:1416756 original size:2 final size:2
Alignment explanation
Indices: 1416749--1416784 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1416739 GTCATTCCCC
1416749 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1416785 GAAGTATATG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1422995 original size:20 final size:20
Alignment explanation
Indices: 1422970--1423062 Score: 96
Period size: 21 Copynumber: 4.5 Consensus size: 20
1422960 TTTTCCCAAT
1422970 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
1422990 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGTAAA
1423010 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGTAAA
* ** *
1423031 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
1423052 TCGCAATGCGA
1 TCGCAATGCGA
1423063 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:1423012 original size:41 final size:41
Alignment explanation
Indices: 1422967--1423062 Score: 183
Period size: 41 Copynumber: 2.3 Consensus size: 41
1422957 CGATTTTCCC
1422967 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1423008 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
*
1423049 AAATCGCAATGCGA
1 AATTCGCAATGCGA
1423063 TACTGACTAT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.19
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
Found at i:1423016 original size:21 final size:20
Alignment explanation
Indices: 1422970--1423062 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
1422960 TTTTCCCAAT
*
1422970 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGGAAA
* **
1422990 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGGAAA
*
1423010 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGGAAA
* **
1423031 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGG-AAA
1423052 TCGCAATGCGA
1 TCGCAATGCGA
1423063 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 29 0.50
21 29 0.50
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGGAAA
Found at i:1423075 original size:41 final size:41
Alignment explanation
Indices: 1422989--1423123 Score: 123
Period size: 41 Copynumber: 3.3 Consensus size: 41
1422979 GAATAAGTAA
* * *
1422989 ATCGCAACGCGAATTGGGAAATTCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
1423030 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * * *
1423071 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
1423112 TTCGCAACGCGA
1 ATCGCAACGCGA
1423124 TACTGACTTT
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
40 4 0.05
41 73 0.92
42 2 0.03
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.20
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:1423076 original size:20 final size:20
Alignment explanation
Indices: 1423051--1423145 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
1423041 AATTGGGAAA
*
1423051 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
1423071 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
1423092 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
1423112 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
1423132 TTCGCAACGCGATA
1 ATCGCAACGCGATA
1423146 ATACATAATC
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.77
21 14 0.23
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:1423650 original size:20 final size:20
Alignment explanation
Indices: 1423625--1423662 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1423615 CGATTCTCTC
1423625 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
1423645 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
1423663 AGAAACTATT
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:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:1424971 original size:18 final size:18
Alignment explanation
Indices: 1424950--1424994 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
1424940 TCCACTTCGG
*
1424950 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
* *
1424968 GAGCTATCACCTCACCTA
1 GAGCCATCACCTCACCCA
1424986 GAGCCATCA
1 GAGCCATCA
1424995 TCTGATCGAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.42, G:0.16, T:0.16
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:1425487 original size:20 final size:20
Alignment explanation
Indices: 1425462--1425507 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
1425452 TAGTTTACTT
1425462 TCGCAACACGAAAATGACTA
1 TCGCAACACGAAAATGACTA
* * *
1425482 TCGCAACGCGGAAATGGCTA
1 TCGCAACACGAAAATGACTA
1425502 TCGCAA
1 TCGCAA
1425508 TGCGAAATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.37, C:0.26, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACACGAAAATGACTA
Found at i:1425524 original size:18 final size:17
Alignment explanation
Indices: 1425501--1425594 Score: 58
Period size: 18 Copynumber: 5.6 Consensus size: 17
1425491 GGAAATGGCT
1425501 ATCGCAATGCGAAATAAA
1 ATCGCAA-GCGAAATAAA
*
1425519 ATCGC-A-CG--ACAAA
1 ATCGCAAGCGAAATAAA
*
1425532 ATCGCAACGCGAAATGAA
1 ATCGCAA-GCGAAATAAA
* *
1425550 ACCGCAA-CG--ACAAA
1 ATCGCAAGCGAAATAAA
1425564 ATCGCAACGCGAAATGAAA
1 ATCGCAA-GCGAAAT-AAA
1425583 ATCGCAATGCGA
1 ATCGCAA-GCGA
1425595 TTTGGTTTCG
Statistics
Matches: 57, Mismatches: 9, Indels: 19
0.67 0.11 0.22
Matches are distributed among these distances:
13 9 0.16
14 10 0.18
15 2 0.04
16 6 0.11
17 1 0.02
18 15 0.26
19 14 0.25
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (17 bp):
ATCGCAAGCGAAATAAA
Found at i:1425544 original size:31 final size:31
Alignment explanation
Indices: 1425501--1425588 Score: 131
Period size: 32 Copynumber: 2.8 Consensus size: 31
1425491 GGAAATGGCT
*
1425501 ATCGCAATGCGAAATAAAATCGCACGACAAA
1 ATCGCAACGCGAAATAAAATCGCACGACAAA
* *
1425532 ATCGCAACGCGAAATGAAACCGCAACGACAAA
1 ATCGCAACGCGAAATAAAATCGC-ACGACAAA
1425564 ATCGCAACGCGAAATGAAAATCGCA
1 ATCGCAACGCGAAAT-AAAATCGCA
1425589 ATGCGATTTG
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
31 20 0.40
32 24 0.48
33 6 0.12
ACGTcount: A:0.47, C:0.25, G:0.18, T:0.10
Consensus pattern (31 bp):
ATCGCAACGCGAAATAAAATCGCACGACAAA
Found at i:1425571 original size:14 final size:14
Alignment explanation
Indices: 1425516--1425572 Score: 53
Period size: 14 Copynumber: 3.9 Consensus size: 14
1425506 AATGCGAAAT
1425516 AAAATCGC-ACGAC
1 AAAATCGCAACGAC
*
1425529 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
*
1425545 ATGAAACCGCAACGAC
1 A--AAATCGCAACGAC
1425561 AAAATCGCAACG
1 AAAATCGCAACG
1425573 CGAAATGAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 9
0.73 0.08 0.19
Matches are distributed among these distances:
13 8 0.23
14 11 0.31
16 8 0.23
18 8 0.23
ACGTcount: A:0.47, C:0.28, G:0.18, T:0.07
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1425583 original size:19 final size:19
Alignment explanation
Indices: 1425529--1425594 Score: 63
Period size: 19 Copynumber: 3.8 Consensus size: 19
1425519 ATCGCACGAC
1425529 AAAATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAATG
* *
1425548 -AAACCGCAA--CG--A-C
1 AAAATCGCAACGCGAAATG
1425561 AAAATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAATG
*
1425580 AAAATCGCAATGCGA
1 AAAATCGCAACGCGA
1425595 TTTGGTTTCG
Statistics
Matches: 36, Mismatches: 5, Indels: 12
0.68 0.09 0.23
Matches are distributed among these distances:
14 9 0.25
16 4 0.11
18 9 0.25
19 14 0.39
ACGTcount: A:0.47, C:0.24, G:0.20, T:0.09
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATG
Found at i:1425611 original size:18 final size:16
Alignment explanation
Indices: 1425590--1425677 Score: 67
Period size: 18 Copynumber: 5.4 Consensus size: 16
1425580 AAAATCGCAA
1425590 TGCGATTTGGTTTCGCGT
1 TGCGATTT--TTTCGCGT
*
1425608 TGCGATTTTGT--CGT
1 TGCGATTTTTTCGCGT
1425622 TGCGATTTCATTTCGCGT
1 TGCGATTT--TTTCGCGT
*
1425640 TGCGATTTTGT--CGT
1 TGCGATTTTTTCGCGT
*
1425654 TGCGATTTTCATTCGCAT
1 TGCGATTTT--TTCGCGT
1425672 TGCGAT
1 TGCGAT
1425678 AGCCATTTCC
Statistics
Matches: 57, Mismatches: 5, Indels: 16
0.73 0.06 0.21
Matches are distributed among these distances:
14 23 0.40
16 7 0.12
18 27 0.47
ACGTcount: A:0.10, C:0.18, G:0.26, T:0.45
Consensus pattern (16 bp):
TGCGATTTTTTCGCGT
Found at i:1425624 original size:14 final size:14
Alignment explanation
Indices: 1425605--1425662 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
1425595 TTTGGTTTCG
1425605 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
1425619 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
1425635 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
1425651 CGTTGCGATTTT
1 CGTTGCGATTTT
1425663 CATTCGCATT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:1425636 original size:32 final size:32
Alignment explanation
Indices: 1425590--1425677 Score: 133
Period size: 32 Copynumber: 2.8 Consensus size: 32
1425580 AAAATCGCAA
**
1425590 TGCGATTTGGTTTCGCGTTGCGATTTTGTCGT
1 TGCGATTTCATTTCGCGTTGCGATTTTGTCGT
1425622 TGCGATTTCATTTCGCGTTGCGATTTTGTCGT
1 TGCGATTTCATTTCGCGTTGCGATTTTGTCGT
*
1425654 TGCGATTTTCA-TTCGCATTGCGAT
1 TGCGA-TTTCATTTCGCGTTGCGAT
1425678 AGCCATTTCC
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
32 47 0.90
33 5 0.10
ACGTcount: A:0.10, C:0.18, G:0.26, T:0.45
Consensus pattern (32 bp):
TGCGATTTCATTTCGCGTTGCGATTTTGTCGT
Found at i:1425696 original size:20 final size:19
Alignment explanation
Indices: 1425665--1425716 Score: 68
Period size: 20 Copynumber: 2.7 Consensus size: 19
1425655 GCGATTTTCA
*
1425665 TTCGCATTGCGATAGCCAT
1 TTCGCGTTGCGATAGCCAT
*
1425684 TTCCGCGTTGCGATAGTCAT
1 TT-CGCGTTGCGATAGCCAT
*
1425704 TTTGCGTTGCGAT
1 TTCGCGTTGCGAT
1425717 TTTAAGTTCG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.15, C:0.23, G:0.25, T:0.37
Consensus pattern (19 bp):
TTCGCGTTGCGATAGCCAT
Found at i:1427087 original size:33 final size:33
Alignment explanation
Indices: 1427045--1427232 Score: 274
Period size: 33 Copynumber: 5.7 Consensus size: 33
1427035 GGAAATTACT
1427045 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
1427078 ATCGCAATGCGAAATGAAAATCGCAAC-ACTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGA-GAGA
* *
1427110 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
1427144 ATCGCAATGCGAAATGAAAATCGCAACGCGA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * *
1427176 TTTGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1427209 ATCGCAATGCGAAATGAAAATCGC
1 ATCGCAATGCGAAATGAAAATCGC
1427233 TACGCGAATT
Statistics
Matches: 137, Mismatches: 13, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
32 30 0.22
33 105 0.77
34 2 0.01
ACGTcount: A:0.43, C:0.19, G:0.23, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:1427212 original size:65 final size:66
Alignment explanation
Indices: 1427046--1427243 Score: 353
Period size: 65 Copynumber: 3.0 Consensus size: 66
1427036 GAAATTACTA
* * *
1427046 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACACTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1427111 T
66 T
1427112 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1427177 T
66 T
*
1427178 T-GCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCTACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1427242 T
66 T
1427243 T
1 T
1427244 AATTTCGCGT
Statistics
Matches: 128, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
65 64 0.50
66 64 0.50
ACGTcount: A:0.41, C:0.19, G:0.23, T:0.17
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:1427258 original size:19 final size:20
Alignment explanation
Indices: 1427236--1427277 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
1427226 AAATCGCTAC
1427236 GCGAATTT-AATTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
*
1427255 GCG-ATTTCATTTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
1427274 GCGA
1 GCGA
1427278 TTCTCTCGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.17, C:0.19, G:0.24, T:0.40
Consensus pattern (20 bp):
GCGAATTTCAATTTCGCGTT
Found at i:1427441 original size:13 final size:13
Alignment explanation
Indices: 1427403--1427445 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
1427393 ATATGTTAAC
1427403 ATCAATTAAACAA
1 ATCAATTAAACAA
* **
1427416 ATCACTTTTACAA
1 ATCAATTAAACAA
1427429 ATCAATTAAAC-A
1 ATCAATTAAACAA
1427441 ATCAA
1 ATCAA
1427446 AAAATAAGCA
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
12 6 0.25
13 18 0.75
ACGTcount: A:0.53, C:0.19, G:0.00, T:0.28
Consensus pattern (13 bp):
ATCAATTAAACAA
Found at i:1428395 original size:33 final size:33
Alignment explanation
Indices: 1428353--1428545 Score: 282
Period size: 33 Copynumber: 5.8 Consensus size: 33
1428343 GGAAATTACT
1428353 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
1428386 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
1428418 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
1428452 ATCGCAATGCGAAATGAAAATCGCAACGCGA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * *
1428484 TTTCACAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1428518 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
1428546 CGAATTTAAT
Statistics
Matches: 141, Mismatches: 15, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
32 2 0.01
33 137 0.97
34 2 0.01
ACGTcount: A:0.42, C:0.20, G:0.23, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:1428460 original size:66 final size:66
Alignment explanation
Indices: 1428354--1428552 Score: 371
Period size: 66 Copynumber: 3.0 Consensus size: 66
1428344 GAAATTACTA
* *
1428354 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1428419 T
66 T
1428420 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1428485 T
66 T
*
1428486 TCACAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1428551 T
66 T
1428552 T
1 T
1428553 AATTTCGCGT
Statistics
Matches: 130, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
66 130 1.00
ACGTcount: A:0.42, C:0.20, G:0.23, T:0.16
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:1428567 original size:19 final size:20
Alignment explanation
Indices: 1428545--1428587 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1428535 AAATCGCAAC
1428545 GCGAATTT-AATTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
* *
1428564 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
1428584 GCGA
1 GCGA
1428588 TTCTCTGTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
GCGAATTTCAATTTCGCGTT
Found at i:1428747 original size:13 final size:13
Alignment explanation
Indices: 1428725--1428756 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
1428715 ATCAATTAAA
1428725 AAATCACTTTTAC
1 AAATCACTTTTAC
*
1428738 AAATCCCTTTTAC
1 AAATCACTTTTAC
1428751 AAATCA
1 AAATCA
1428757 ATTAAACAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.41, C:0.25, G:0.00, T:0.34
Consensus pattern (13 bp):
AAATCACTTTTAC
Found at i:1430006 original size:21 final size:21
Alignment explanation
Indices: 1429940--1430006 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1429930 GTGAATCGGG
1429940 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAATGGTGGGAGGGGA
* * * ** * *
1429960 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAATGGTGGGAGGGGA
1429982 CTCTTGAATGGTGGGAGGGGA
1 CTCTTGAATGGTGGGAGGGGA
1430003 CTCT
1 CTCT
1430007 CGAGGAATGA
Statistics
Matches: 31, Mismatches: 14, Indels: 2
0.66 0.30 0.04
Matches are distributed among these distances:
21 29 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.19, G:0.36, T:0.25
Consensus pattern (21 bp):
CTCTTGAATGGTGGGAGGGGA
Found at i:1432093 original size:20 final size:19
Alignment explanation
Indices: 1432062--1432241 Score: 128
Period size: 19 Copynumber: 9.8 Consensus size: 19
1432052 TCTTTTGGTT
1432062 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
1432081 GATAATGAGAATCGCAACGCG
1 GA-AATGAAAATCGCAACG-A
**
1432102 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
1432121 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
** * *
1432135 GAAATGACTATCGCGACCA
1 GAAATGAAAATCGCAACGA
* *
1432154 GACA-G----TCGCAACGC
1 GAAATGAAAATCGCAACGA
*
1432168 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGA
* *
1432188 GAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGA
*
1432207 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGA
1432226 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
1432242 TGCGATTTTG
Statistics
Matches: 130, Mismatches: 18, Indels: 26
0.75 0.10 0.15
Matches are distributed among these distances:
14 19 0.15
15 1 0.01
16 2 0.02
17 2 0.02
18 1 0.01
19 56 0.43
20 47 0.36
21 2 0.02
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:1432144 original size:33 final size:33
Alignment explanation
Indices: 1432087--1432185 Score: 135
Period size: 33 Copynumber: 3.0 Consensus size: 33
1432077 ACGAGATAAT
*
1432087 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
*
1432121 GAGAATCGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
* * **
1432154 GACAGTCGCAACGCGAAATGAAAATCGCAACC
1 GAGAATCGCAACGCGAAATGACTATCGCAACC
1432186 GCGAAATAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
33 44 0.76
34 14 0.24
ACGTcount: A:0.38, C:0.26, G:0.24, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:1432181 original size:19 final size:19
Alignment explanation
Indices: 1432159--1432246 Score: 149
Period size: 19 Copynumber: 4.6 Consensus size: 19
1432149 GACCAGACAG
1432159 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1432178 TCGCAACCGCGAAATAAAAA
1 TCGCAA-CGCGAAATGAAAA
1432198 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
1432217 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1432236 TCGCAATGCGA
1 TCGCAACGCGA
1432247 TTTTGGTTTC
Statistics
Matches: 65, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
19 47 0.72
20 18 0.28
ACGTcount: A:0.45, C:0.23, G:0.20, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:1432202 original size:39 final size:38
Alignment explanation
Indices: 1432159--1432246 Score: 149
Period size: 39 Copynumber: 2.3 Consensus size: 38
1432149 GACCAGACAG
1432159 TCGCAACGCGAAATGAAAATCGCAACCGCGAAATAAAAA
1 TCGCAACGCGAAATGAAAATCGCAA-CGCGAAATAAAAA
*
1432198 TCGCAACGCGAAATGAAAATCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAATCGCAACGCGAAATAAAAA
*
1432236 TCGCAATGCGA
1 TCGCAACGCGA
1432247 TTTTGGTTTC
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
38 22 0.47
39 25 0.53
ACGTcount: A:0.45, C:0.23, G:0.20, T:0.11
Consensus pattern (38 bp):
TCGCAACGCGAAATGAAAATCGCAACGCGAAATAAAAA
Found at i:1432275 original size:19 final size:19
Alignment explanation
Indices: 1432242--1432308 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
1432232 AAAATCGCAA
**
1432242 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
*
1432261 TGCGATTTTTATTTCTCGT
1 TGCGATTTTTATTTCGCGT
**
1432280 TGCGATAGTTATTTCCGCGT
1 TGCGATTTTTATTT-CGCGT
1432300 TGCGATTTT
1 TGCGATTTT
1432309 CATTCTCGAA
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 28 0.72
20 11 0.28
ACGTcount: A:0.10, C:0.16, G:0.24, T:0.49
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:1432845 original size:20 final size:20
Alignment explanation
Indices: 1432820--1432913 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
1432810 CGCTATGTAA
1432820 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGAAAGTCAGT
*
1432840 ATCGCGTTGCGAAAGTAAGT
1 ATCGCGTTGCGAAAGTCAGT
* *** * *
1432860 ATCTCGTTGCGATTTTTTATT
1 ATCGCGTTGCGA-AAGTCAGT
* *
1432881 ATCGCATTGCGATAGTCAGT
1 ATCGCGTTGCGAAAGTCAGT
*
1432901 ATCGCATTGCGAA
1 ATCGCGTTGCGAA
1432914 TTTCCCAATT
Statistics
Matches: 59, Mismatches: 14, Indels: 2
0.79 0.19 0.03
Matches are distributed among these distances:
20 46 0.78
21 13 0.22
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.33
Consensus pattern (20 bp):
ATCGCGTTGCGAAAGTCAGT
Found at i:1432931 original size:21 final size:21
Alignment explanation
Indices: 1432902--1432956 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 21
1432892 ATAGTCAGTA
*
1432902 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCGAATTTACCAAT
* **
1432923 TCGCGTTGCG-ATTTACTTAT
1 TCGCATTGCGAATTTACCAAT
1432943 TCGCATTGCGAATT
1 TCGCATTGCGAATT
1432957 GGGAAAATCG
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
20 16 0.57
21 12 0.43
ACGTcount: A:0.20, C:0.24, G:0.18, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGAATTTACCAAT
Found at i:1437385 original size:181 final size:183
Alignment explanation
Indices: 1437049--1437524 Score: 695
Period size: 182 Copynumber: 2.6 Consensus size: 183
1437039 GATCCAAATT
* * * **
1437049 AAAAATGTGTCGATCCAAAACGATATAACAGGTAAAACTATGACAAAACCGGTATTGAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
* * * * *
1437114 AAACCGGTAAAGCGCTACCGGATACATTTAAAGTGTCGGTACTTTAATATAAGGATCGACACTTC
66 AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
* *
1437179 GTGAATTTAAAAGAGAAACAGTTTTAAATCCTATAAAGTGTCGATACTTT-TA
131 GTGAATTTAAAAGAGAAACAGTTTTAAAGCCTATAAAGTGTCGATACTTTAAA
* * *
1437231 AAAAATGTATCGATCCAAAATGATATACCAGGTAAAAATATGATAAAACCGATATCAAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
* * *
1437296 AAACCGGTAAAATGTTACCGGATATATTGAAAGTGTCGATACTTT-ATATAAGGATCGACACTTT
66 AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
* ** *
1437360 GTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAATGTGTCGATACTTTAAA
131 GTGAATTTAAAAGAGAAACAGTTTTAAAGCCTATAAAGTGTCGATACTTTAAA
* * *
1437413 AAAATATATATCGATCCACAACGATATAACATGTAAAAATATGATAAAACCGGTATCAAAATGAT
1 AAAA-ATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGAT
1437478 AAAAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTT
65 -AAAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTT
1437525 CGTAAGTACG
Statistics
Matches: 262, Mismatches: 29, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
181 63 0.24
182 101 0.39
183 54 0.21
184 44 0.17
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.27
Consensus pattern (183 bp):
AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
GTGAATTTAAAAGAGAAACAGTTTTAAAGCCTATAAAGTGTCGATACTTTAAA
Found at i:1439734 original size:21 final size:21
Alignment explanation
Indices: 1439708--1439772 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
1439698 AAGATAATCA
*
1439708 AGAGTCGAAGAGAAACTTGAT
1 AGAGTCGAAGAGAAACTTGAG
1439729 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
* *
1439750 AGAGTCGAAGATACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
1439771 AG
1 AG
1439773 GCATAAGGGG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.42, C:0.11, G:0.31, T:0.17
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:1439848 original size:33 final size:33
Alignment explanation
Indices: 1439806--1439871 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
1439796 AAATAGATGG
*
1439806 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
1439839 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
1439872 TATTAAGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.48, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:1441690 original size:19 final size:19
Alignment explanation
Indices: 1441666--1441712 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
1441656 AATGTAGGGT
1441666 TAATTTTGTATA-AGATTTA
1 TAATTTTGTATACA-ATTTA
1441685 TAATTTTGTATACAATTTA
1 TAATTTTGTATACAATTTA
1441704 TAATTTTGT
1 TAATTTTGT
1441713 GTGTGAATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 26 0.96
20 1 0.04
ACGTcount: A:0.34, C:0.02, G:0.09, T:0.55
Consensus pattern (19 bp):
TAATTTTGTATACAATTTA
Found at i:1442296 original size:200 final size:200
Alignment explanation
Indices: 1441948--1443111 Score: 2026
Period size: 200 Copynumber: 5.8 Consensus size: 200
1441938 AATTTACAAT
*
1441948 ATGGCAAACAGGGTGCAACCATAAAGTGTC-ATTCCATATATAAAAAGTGTCGATCCCATAAACA
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGA-TCCATATATAAAAAGTGTCGATCCCATAAACA
* * *
1442012 TCGAAACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAATCGGTACAAGTATATCGGTTT
65 TCGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTT
*
1442077 TATGAGAGAATATGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCA
130 TATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCA
1442142 GAATGA
195 GAATGA
* * *
1442148 ATGGCAAACAGGGTGCAACAATAAAGTGTTGATCTATATATAAAAAGTGTCGATCCGATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
* *
1442213 CGAAACCTATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGATACAAGTATACCGGTTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
* **
1442278 AAGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTAAATATTTTTGGTCCAG
131 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
1442343 AATGA
196 AATGA
*
1442348 ATGGCAAACAGGGTGCAACAATAAAGTGTTGATCCATATATAAAAAGTGTCGATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
*
1442413 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAATCGGTACAAGTATACCGGTTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
1442478 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
131 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
1442543 AATGA
196 AATGA
1442548 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
* *
1442613 CGAAACCTATAAGTATAATGTAATAGGCAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
1442678 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
131 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
1442743 AATGA
196 AATGA
*
1442748 ATGACAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
*
1442813 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAATCGGTACAAGTATACCGGTTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
*
1442878 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAG
131 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
1442943 AATGA
196 AATGA
* *
1442948 ATGGAAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
* * * * *
1443013 CAAAACCCAAAAGTATAATGTATTAGGTAATTTTTCAATCTAACCGGTATAAGTATACCAGTTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
* * *
1443078 ATGGGAGAATTGGTATATAAT-ATGTATCGACACT
131 ATGAGAGAATAGGTCTA-AATAATGTATCGACACT
1443112 GTTTAATGTT
Statistics
Matches: 920, Mismatches: 42, Indels: 4
0.95 0.04 0.00
Matches are distributed among these distances:
200 916 1.00
201 4 0.00
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.31
Consensus pattern (200 bp):
ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
AATGA
Found at i:1444575 original size:6 final size:6
Alignment explanation
Indices: 1444564--1444631 Score: 82
Period size: 6 Copynumber: 11.3 Consensus size: 6
1444554 CAAGCGGTCA
* * * * * *
1444564 ATGAAG ATGAAG ATGACG ATGAAG ATGACG ATGATG ACGATG ATGATG
1 ATGATG ATGATG ATGATG ATGATG ATGATG ATGATG ATGATG ATGATG
1444612 ATGATG ATGATG ATGATG AT
1 ATGATG ATGATG ATGATG AT
1444632 CCAAACAAGT
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 56 1.00
ACGTcount: A:0.38, C:0.04, G:0.32, T:0.25
Consensus pattern (6 bp):
ATGATG
Found at i:1444628 original size:9 final size:9
Alignment explanation
Indices: 1444564--1444631 Score: 82
Period size: 9 Copynumber: 7.6 Consensus size: 9
1444554 CAAGCGGTCA
*
1444564 ATGAAGATG
1 ATGATGATG
* *
1444573 AAGATGACG
1 ATGATGATG
*
1444582 ATGAAGATG
1 ATGATGATG
*
1444591 ACGATGATG
1 ATGATGATG
*
1444600 ACGATGATG
1 ATGATGATG
1444609 ATGATGATG
1 ATGATGATG
1444618 ATGATGATG
1 ATGATGATG
1444627 ATGAT
1 ATGAT
1444632 CCAAACAAGT
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 50 1.00
ACGTcount: A:0.38, C:0.04, G:0.32, T:0.25
Consensus pattern (9 bp):
ATGATGATG
Found at i:1446328 original size:121 final size:120
Alignment explanation
Indices: 1446114--1446361 Score: 406
Period size: 121 Copynumber: 2.1 Consensus size: 120
1446104 ACATCGGAAC
* * *
1446114 CCAGAATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGC
1 CCAGAATTATAATATAATAGATAATCTTGTAATATAACCGGTATAAATATACCGATTTTATGAGC
*
1446179 GAATAGGTCTACAACCTATATCGACACTTTTTTAATTTTGTGTCAGTACTTTATGT
66 GAATAGGTCTACAACCTATATCGACAC-TTTTTAATATTGTGTCAGTACTTTATGT
* * *
1446235 CCAGAATTATAATATACTAGATAATCTTGTAATATAACCGGTATAAGTATACCGATTTTATTAGC
1 CCAGAATTATAATATAATAGATAATCTTGTAATATAACCGGTATAAATATACCGATTTTATGAGC
* *
1446300 GAATAGGTCTACAACCTATGTCGACACTTTTTAATATTGTGTCGGTACTTTATGT
66 GAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCAGTACTTTATGT
1446355 CCAGAAT
1 CCAGAAT
1446362 GGAAGAAAAA
Statistics
Matches: 118, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
120 33 0.28
121 85 0.72
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.38
Consensus pattern (120 bp):
CCAGAATTATAATATAATAGATAATCTTGTAATATAACCGGTATAAATATACCGATTTTATGAGC
GAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCAGTACTTTATGT
Found at i:1446631 original size:120 final size:120
Alignment explanation
Indices: 1446418--1446664 Score: 413
Period size: 120 Copynumber: 2.1 Consensus size: 120
1446408 ACATCGGAAC
*
1446418 CCAGAATTATAATGTAATAGATAATTTTGTAATATAACCGATATAAATATACCGGTTTTATGAGT
1 CCAGAATTATAATGTAATAGATAATTTTGTAATATAACCGATATAAATATACCGGTTTTATGAGC
**
1446483 GAATAGGTCTACAACCTATATCGACACTTTTTAATTTTGTGTCGGTACTTTATGT
66 GAATAGGTCTACAACCTATATCGACACTTTTTAATAATGTGTCGGTACTTTATGT
* * * *
1446538 CCAGAATTATAATGTACTAGATAATTTTGTAATATAACCGGTATAAGTATACCGGTTTTATTAGC
1 CCAGAATTATAATGTAATAGATAATTTTGTAATATAACCGATATAAATATACCGGTTTTATGAGC
* *
1446603 GAATAGGTCTATAACCTATGTCGACACTTTTTAATAATGTGTCGGTACTTTATGT
66 GAATAGGTCTACAACCTATATCGACACTTTTTAATAATGTGTCGGTACTTTATGT
1446658 CCAGAAT
1 CCAGAAT
1446665 GGAAGAAAAA
Statistics
Matches: 118, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
120 118 1.00
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.38
Consensus pattern (120 bp):
CCAGAATTATAATGTAATAGATAATTTTGTAATATAACCGATATAAATATACCGGTTTTATGAGC
GAATAGGTCTACAACCTATATCGACACTTTTTAATAATGTGTCGGTACTTTATGT
Found at i:1446665 original size:303 final size:303
Alignment explanation
Indices: 1445951--1447131 Score: 2157
Period size: 303 Copynumber: 3.9 Consensus size: 303
1445941 ATATAATGTA
* * * * * *
1445951 ATAATTTTGTAATATAATCGGTATAAATATACCAGTTTTATGAGCGAATATGTCTACAACCTATA
1 ATAATTTTGTAATATAACCGGTATAAGTATACCGGTTTTATTAGCGAATAGGTCTACAACCTATG
* *
1446016 TCGACACTTTTTAATATTGTGTTGGTACTTTATGTCCAGAATAGAAGAAAAATGTGTCGATACCT
66 TCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCT
1446081 TGTCAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAA
131 TGTCAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAA
1446146 TATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTTT
196 TATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACAC-TTTT
* *
1446211 TAATTTTGTGTCAGTACTTTATGTCCAGAATTATAATATACTAG
260 TAATTTTGTGTCGGTACTTTATGTCCAGAATTATAATGTACTAG
* *
1446255 ATAATCTTGTAATATAACCGGTATAAGTATACCGATTTTATTAGCGAATAGGTCTACAACCTATG
1 ATAATTTTGTAATATAACCGGTATAAGTATACCGGTTTTATTAGCGAATAGGTCTACAACCTATG
1446320 TCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCT
66 TCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCT
1446385 TGTCAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAA
131 TGTCAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAA
* *
1446450 TATAACCGATATAAATATACCGGTTTTATGAGTGAATAGGTCTACAACCTATATCGACACTTTTT
196 TATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTTT
1446515 AATTTTGTGTCGGTACTTTATGTCCAGAATTATAATGTACTAG
261 AATTTTGTGTCGGTACTTTATGTCCAGAATTATAATGTACTAG
*
1446558 ATAATTTTGTAATATAACCGGTATAAGTATACCGGTTTTATTAGCGAATAGGTCTATAACCTATG
1 ATAATTTTGTAATATAACCGGTATAAGTATACCGGTTTTATTAGCGAATAGGTCTACAACCTATG
*
1446623 TCGACACTTTTTAATAATGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCT
66 TCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCT
1446688 TGTCAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAA
131 TGTCAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAA
1446753 TATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTTT
196 TATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTTT
*
1446818 AATTTTGTGTCGGTACTTTATGTACAGAATTATAATGTACTAG
261 AATTTTGTGTCGGTACTTTATGTCCAGAATTATAATGTACTAG
1446861 ATAATTTTGTAATATAACCGGTATAAGTATACCGGTTTTATTAGCGAATAGGTCTACAACCTATG
1 ATAATTTTGTAATATAACCGGTATAAGTATACCGGTTTTATTAGCGAATAGGTCTACAACCTATG
1446926 TCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCT
66 TCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCT
* *
1446991 TGTCAAAAAGTGTCGACATTTACACATCGGAACCCAAAATTATAATGTCATAGATAATTTT-TAA
131 TGTCAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAA
*
1447055 TATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGATACTTTTT
196 TATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTTT
*
1447120 AATATTGTGTCG
261 AATTTTGTGTCG
1447132 CTAATTTTAA
Statistics
Matches: 850, Mismatches: 27, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
302 78 0.09
303 529 0.62
304 243 0.29
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (303 bp):
ATAATTTTGTAATATAACCGGTATAAGTATACCGGTTTTATTAGCGAATAGGTCTACAACCTATG
TCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCT
TGTCAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAA
TATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTTT
AATTTTGTGTCGGTACTTTATGTCCAGAATTATAATGTACTAG
Found at i:1446935 original size:120 final size:120
Alignment explanation
Indices: 1446722--1446967 Score: 438
Period size: 120 Copynumber: 2.0 Consensus size: 120
1446712 CATCGGAACC
1446722 CAGAATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCG
1 CAGAATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCG
*
1446787 AATAGGTCTACAACCTATATCGACACTTTTTAATTTTGTGTCGGTACTTTATGTA
66 AATAGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTA
* * *
1446842 CAGAATTATAATGTACTAGATAATTTTGTAATATAACCGGTATAAGTATACCGGTTTTATTAGCG
1 CAGAATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCG
* *
1446907 AATAGGTCTACAACCTATGTCGACACTTTTTAATATTGTGTCGGTACTTTATGTC
66 AATAGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTA
1446962 CAGAAT
1 CAGAAT
1446968 GGAAGAAAAA
Statistics
Matches: 120, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
120 120 1.00
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.38
Consensus pattern (120 bp):
CAGAATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCG
AATAGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTA
Found at i:1449925 original size:23 final size:23
Alignment explanation
Indices: 1449894--1449966 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
1449884 ATAGGTAAAA
*
1449894 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
*
1449917 ATATAATGTAATAGGTAGCGTTT
1 ATATAATGTAATAGGTAGCGCTT
*
1449940 ATATAATGTAATAGGTAGTGCTT
1 ATATAATGTAATAGGTAGCGCTT
1449963 ATAT
1 ATAT
1449967 TGTAAAGTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.34, C:0.05, G:0.22, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:1450403 original size:23 final size:23
Alignment explanation
Indices: 1450372--1450444 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
1450362 ATAGGTAAAA
*
1450372 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
*
1450395 ATATAATGTAATAGGTAGCGTTT
1 ATATAATGTAATAGGTAGCGCTT
*
1450418 ATATAATGTAATAGGTAGTGCTT
1 ATATAATGTAATAGGTAGCGCTT
1450441 ATAT
1 ATAT
1450445 TGTAAAGTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.34, C:0.05, G:0.22, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:1450579 original size:478 final size:478
Alignment explanation
Indices: 1449682--1451795 Score: 3724
Period size: 478 Copynumber: 4.4 Consensus size: 478
1449672 GGTGCACGCA
*
1449682 TAATATTGTTAAATTTCAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
1 TAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
* * * *
1449747 TGTGTAAATGAAATTATTAAATTAATATTTTAGGCGGAAAACATGAAATACTATTAAAAAATAAA
66 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAA-AAT
1449812 TGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCATTTTTATAAAAAGTATGGACACTTT
130 TGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCATTTTTATAAAAAGTATGGACACTTT
1449877 CAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTAGCGTTTAT
195 CAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTAGCGTTTAT
*
1449942 ATAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTATTCTTTTTATAAAAGTGTCCATACTTT
260 ATAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTT
1450007 TTTCACTGTGGAAAACATTAATTTAAGGTTAGTTTTAAGATATTAATTTAGTAATTATAGGCGTC
325 TTTCACTGTGGAAAACATTAATTTAAGGTTAGTTTTAAGATATTAATTTAGTAATTATAGGCGTC
1450072 TAATGATTTATTTTTTACGTTACGGTATATATTATTATTAAATTAAAAACAATAAACATATATAT
390 TAATGATTTATTTTTTACGTTACGGTATATATTATTATTAAATTAAAAACAATAAACATATATAT
1450137 TACATATTTATTATTATCTTTGGT
455 TACATATTTATTATTATCTTTGGT
*
1450161 TAATATTATTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
1 TAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
1450226 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATT
66 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATT
* *
1450291 GAAACATAAATTGCATAACTTTAAAAAAAATATCGATCATTTTTATAAAAAGTATGGACACTTTC
131 GAAACATAAATTACATAACTTTAAAAAAAGTATCGATCATTTTTATAAAAAGTATGGACACTTTC
1450356 AATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTAGCGTTTATA
196 AATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTAGCGTTTATA
1450421 TAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTTT
261 TAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTTT
1450486 TTCACTGTGGAAAACATTAATTTAAGGTTAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCT
326 TTCACTGTGGAAAACATTAATTTAAGGTTAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCT
1450551 AATGATTTATTTTTTACGTTACGGTATATATTATTATTAAATTAAAAACAATAAACATATATATT
391 AATGATTTATTTTTTACGTTACGGTATATATTATTATTAAATTAAAAACAATAAACATATATATT
1450616 ACATATTTATTATTATCTTTGGT
456 ACATATTTATTATTATCTTTGGT
*
1450639 TAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAAAAATCAAATAATTTTT
1 TAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAA-TTTT
1450704 TTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAAT
65 TTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAAT
* *
1450769 TGAAACATAAATTACATAACTTTAAAAAAAGTATCAATCCTTTTTATAAAAA-TATGGACACTTT
130 TGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCATTTTTATAAAAAGTATGGACACTTT
* *
1450833 CAATATAATAGATAAAAATATGATGTAATAGGTAGCACTTATATAATGTAATAGGTAGCGTTTAT
195 CAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTAGCGTTTAT
*
1450898 ATAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCAATACTTT
260 ATAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTT
*
1450963 TTTCACTGTGGAAAACATTAATTTAAGGTTAGTTTTAAAATATTAATTTAGTAATTATAGGCGTC
325 TTTCACTGTGGAAAACATTAATTTAAGGTTAGTTTTAAGATATTAATTTAGTAATTATAGGCGTC
1451028 TAATGATTTA-TTTTTACGTTACGGTATATATTATTATTAAATT-AAAA-AATAAAC--ATATAT
390 TAATGATTTATTTTTTACGTTACGGTATATATTATTATTAAATTAAAAACAATAAACATATATAT
1451088 TACATATTTATTATTATCTTTGGT
455 TACATATTTATTATTATCTTTGGT
*
1451112 TAATATTATTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
1 TAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
*
1451177 TGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATT
66 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATT
* * *
1451242 GAAACATAAATTGCATAACTTT-AAAAAAGTATCGATCTTTTTTATAAAAAGTATGAACACTTTC
131 GAAACATAAATTACATAACTTTAAAAAAAGTATCGATCATTTTTATAAAAAGTATGGACACTTTC
*
1451306 AATATAATAGGTAAAAATATGATGTAATATGTAGCGCTTATATAATGTAATAGGTAGCGTTTATA
196 AATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTAGCGTTTATA
*
1451371 TAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTATCATTTTTATAAAAGTGTCCATACTTTT
261 TAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTTT
* *
1451436 TTCAATGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATCAATTTAGTAA
326 TTCACTGTGGAAAACATTAATTTAAGG--------T---T-AGTTTTAAGATATTAATTTAGTAA
**** * *
1451501 TTATATATATCTAATGATTTATTTTTTATGTTACGGTATATATTATCATTAAATTAAAAACAATA
379 TTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATTATTAAATTAAAAACAATA
*
1451566 AACATATATATTACATATTTATTATTATCTTTAGT
444 AACATATATATTACATATTTATTATTATCTTTGGT
*
1451601 TAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTT
1 TAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
* *
1451666 TGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAATACTATT--AAAAAATT
66 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATT
1451729 GAAACATAAATTACATAACTTTAAAAAAAGTATCGATCATTTTTATAAAAAGTATGGACACTTTC
131 GAAACATAAATTACATAACTTTAAAAAAAGTATCGATCATTTTTATAAAAAGTATGGACACTTTC
1451794 AA
196 AA
1451796 CATATTATAA
Statistics
Matches: 1568, Mismatches: 47, Indels: 31
0.95 0.03 0.02
Matches are distributed among these distances:
471 26 0.02
472 253 0.16
473 88 0.06
475 7 0.00
476 4 0.00
477 33 0.02
478 619 0.39
479 238 0.15
480 1 0.00
483 1 0.00
484 39 0.02
485 31 0.02
486 4 0.00
487 36 0.02
488 42 0.03
489 146 0.09
ACGTcount: A:0.42, C:0.07, G:0.11, T:0.40
Consensus pattern (478 bp):
TAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATT
GAAACATAAATTACATAACTTTAAAAAAAGTATCGATCATTTTTATAAAAAGTATGGACACTTTC
AATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTAGCGTTTATA
TAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTTT
TTCACTGTGGAAAACATTAATTTAAGGTTAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCT
AATGATTTATTTTTTACGTTACGGTATATATTATTATTAAATTAAAAACAATAAACATATATATT
ACATATTTATTATTATCTTTGGT
Found at i:1450881 original size:23 final size:23
Alignment explanation
Indices: 1450850--1450922 Score: 110
Period size: 23 Copynumber: 3.2 Consensus size: 23
1450840 ATAGATAAAA
* *
1450850 ATATGATGTAATAGGTAGCACTT
1 ATATAATGTAATAGGTAGCGCTT
*
1450873 ATATAATGTAATAGGTAGCGTTT
1 ATATAATGTAATAGGTAGCGCTT
*
1450896 ATATAATGTAATAGGTAGTGCTT
1 ATATAATGTAATAGGTAGCGCTT
1450919 ATAT
1 ATAT
1450923 TGTAAAGTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.36, C:0.05, G:0.21, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:1451353 original size:23 final size:23
Alignment explanation
Indices: 1451322--1451394 Score: 110
Period size: 23 Copynumber: 3.2 Consensus size: 23
1451312 ATAGGTAAAA
* *
1451322 ATATGATGTAATATGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
*
1451345 ATATAATGTAATAGGTAGCGTTT
1 ATATAATGTAATAGGTAGCGCTT
*
1451368 ATATAATGTAATAGGTAGTGCTT
1 ATATAATGTAATAGGTAGCGCTT
1451391 ATAT
1 ATAT
1451395 TGTAAAGTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:1457463 original size:9 final size:9
Alignment explanation
Indices: 1457440--1457558 Score: 59
Period size: 9 Copynumber: 12.8 Consensus size: 9
1457430 AGATCCAATC
1457440 AGAAAAAAGA
1 AGAAAAAA-A
1457450 AGAAAAAAA
1 AGAAAAAAA
*
1457459 GGAAAAAAA
1 AGAAAAAAA
*
1457468 A-AAGAAAA
1 AGAAAAAAA
* *
1457476 AG-AAATAG
1 AGAAAAAAA
*
1457484 AGCAAAAAA
1 AGAAAAAAA
*
1457493 AG--AGAAA
1 AGAAAAAAA
1457500 AGAAAAAAA
1 AGAAAAAAA
1457509 AGAAATTAAAGCAA
1 AG-AA--AAA--AA
1457523 AGAAAAAAA
1 AGAAAAAAA
1457532 GAGCAAAAAAGA
1 -AG-AAAAAA-A
*
1457544 A-AAGAAAA
1 AGAAAAAAA
1457552 AGAAAAA
1 AGAAAAA
1457559 GGGACGATAA
Statistics
Matches: 84, Mismatches: 12, Indels: 27
0.68 0.10 0.22
Matches are distributed among these distances:
7 6 0.07
8 14 0.17
9 32 0.38
10 12 0.14
11 10 0.12
12 4 0.05
13 2 0.02
14 4 0.05
ACGTcount: A:0.78, C:0.03, G:0.17, T:0.03
Consensus pattern (9 bp):
AGAAAAAAA
Found at i:1457468 original size:23 final size:22
Alignment explanation
Indices: 1457442--1457557 Score: 72
Period size: 23 Copynumber: 4.7 Consensus size: 22
1457432 ATCCAATCAG
1457442 AAAAAAGAAGAAAAAAAGGAAAA
1 AAAAAAGAA-AAAAAAAGGAAAA
1457465 AAAAAAGAAAAAGAAATAGAGCAAAA
1 AAAAAAGAAAAA-AAA-AG-G-AAAA
*
1457491 AAAGAGAA-AAGAAAAAAAAGAAATTA
1 AAA-A-AAGAA-AAAAAAAGGAAA--A
* * *
1457517 AAGCAAAGAAAAAAAGAGCAAAA
1 AA-AAAAGAAAAAAAAAGGAAAA
1457540 AAGAAAAGAAAAAGAAAA
1 AA-AAAAGAAAAA-AAAA
1457558 AGGGACGATA
Statistics
Matches: 74, Mismatches: 7, Indels: 23
0.71 0.07 0.22
Matches are distributed among these distances:
22 3 0.04
23 25 0.34
24 8 0.11
25 13 0.18
26 14 0.19
27 6 0.08
28 5 0.07
ACGTcount: A:0.78, C:0.03, G:0.16, T:0.03
Consensus pattern (22 bp):
AAAAAAGAAAAAAAAAGGAAAA
Found at i:1457522 original size:34 final size:35
Alignment explanation
Indices: 1457452--1457556 Score: 97
Period size: 34 Copynumber: 2.8 Consensus size: 35
1457442 AAAAAAGAAG
*
1457452 AAAAAAAGGAAAAAAAAAAGAAAAAGAAATAGAGC
1 AAAAAAAGGAAAAAAAAAAGAAAAAGAAATAAAGC
* *
1457487 AAAAAAA-GAGAAAAGAAA-AAAAAGAAATTAAAGC
1 AAAAAAAGGAAAAAAAAAAGAAAAAGAAA-TAAAGC
1457521 AAAGAAAAAAAGAGCAAAAAAGAAAAGAAAAAGAAA
1 ----AAAAAAAG-G-AAAAAA-AAAAGAAAAAGAAA
1457557 AAGGGACGAT
Statistics
Matches: 55, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
33 9 0.16
34 14 0.25
35 7 0.13
38 7 0.13
40 1 0.02
41 5 0.09
42 3 0.05
43 9 0.16
ACGTcount: A:0.78, C:0.03, G:0.16, T:0.03
Consensus pattern (35 bp):
AAAAAAAGGAAAAAAAAAAGAAAAAGAAATAAAGC
Found at i:1457538 original size:15 final size:15
Alignment explanation
Indices: 1457518--1457558 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
1457508 AAGAAATTAA
1457518 AGCAAAGAAAAAAAG
1 AGCAAAGAAAAAAAG
1457533 AGCAAA-AAAGAAAAG
1 AGCAAAGAAA-AAAAG
*
1457548 A-AAAAGAAAAA
1 AGCAAAGAAAAA
1457559 GGGACGATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
14 8 0.35
15 15 0.65
ACGTcount: A:0.78, C:0.05, G:0.17, T:0.00
Consensus pattern (15 bp):
AGCAAAGAAAAAAAG
Found at i:1457540 original size:33 final size:32
Alignment explanation
Indices: 1457472--1457545 Score: 80
Period size: 33 Copynumber: 2.3 Consensus size: 32
1457462 AAAAAAAAAG
*
1457472 AAAAAGAAATAGAGCAAAAAAAGAGAAAAGAAA
1 AAAAAGAAATAAAGCAAAAAAAGAGAAAAG-AA
* *
1457505 AAAAAGAAATTAAAGCAAAGAAAA-A-AAGAGCA
1 AAAAAGAAA-TAAAGCAAA-AAAAGAGAAAAGAA
1457537 AAAAAGAAA
1 AAAAAGAAA
1457546 AGAAAAAGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
32 10 0.28
33 13 0.36
34 9 0.25
35 4 0.11
ACGTcount: A:0.76, C:0.04, G:0.16, T:0.04
Consensus pattern (32 bp):
AAAAAGAAATAAAGCAAAAAAAGAGAAAAGAA
Found at i:1458620 original size:30 final size:32
Alignment explanation
Indices: 1458585--1458658 Score: 100
Period size: 31 Copynumber: 2.4 Consensus size: 32
1458575 GCATCGTTAA
*
1458585 AGATTCAACA-CAAATGTTGGGGCATA-TTGG
1 AGATTCAACATCAAATATTGGGGCATATTTGG
*
1458615 AGATTCAACATCGAATATTGGGGCATATTTGG
1 AGATTCAACATCAAATATTGGGGCATATTTGG
1458647 -GAATTCAACATC
1 AG-ATTCAACATC
1458659 TTGATGCAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
30 10 0.26
31 15 0.38
32 14 0.36
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.28
Consensus pattern (32 bp):
AGATTCAACATCAAATATTGGGGCATATTTGG
Found at i:1459488 original size:41 final size:41
Alignment explanation
Indices: 1459383--1459508 Score: 141
Period size: 41 Copynumber: 3.0 Consensus size: 41
1459373 ACGAATGGGC
* *
1459383 CATCCACGATTTCAACTCCATGACAGAGGATATCGTACCACG
1 CATCCACGATTTCAACTCCACGACAGAGGA-ATCGTACCACA
* *
1459425 GATCCACGATTTCAACTCCACGACAGAGG-ATCGTGCCCACA
1 CATCCACGATTTCAACTCCACGACAGAGGAATCGT-ACCACA
* *
1459466 CATCCACGGTTTCAACTTCACGAC-GAAGGGAATCGTA-CACA
1 CATCCACGATTTCAACTCCACGACAG-A-GGAATCGTACCACA
1459507 CA
1 CA
1459509 AGTAGCATCC
Statistics
Matches: 72, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
40 6 0.08
41 32 0.44
42 29 0.40
43 5 0.07
ACGTcount: A:0.31, C:0.32, G:0.18, T:0.19
Consensus pattern (41 bp):
CATCCACGATTTCAACTCCACGACAGAGGAATCGTACCACA
Found at i:1459602 original size:332 final size:334
Alignment explanation
Indices: 1458896--1459685 Score: 1207
Period size: 332 Copynumber: 2.4 Consensus size: 334
1458886 CTCAACTTCA
* *
1458896 CAAAGAATGAGTGTCTGTC-ATAAACTTTCCAGTTTCATAGCCAATTTCAACTTCACGACGAAGG
1 CAAAGAAAGAGTGTCTGTCAATAAACTTTCCAGTTTCAGAGCCAATTTCAACTTCACGACGAAGG
* * * *
1458960 ATATTGGACTCGAAATAGCACAAGCTTAGATTTCAACTTCACAACGAATGATATTCAAGTCAAGG
66 ATATTGGACTCGAAACAGCACAAGCTTGGATTTCAACTTCACGACGAAGGATATTCAAGTCAAGG
* *
1459025 CTCAACTTCACGATGAAGGGGCCATCCACGATTTCAACTCCACGACGGAGGAGGATCGTACCAAC
131 CTCAACTTCACGACGAAGGGGCCATCCACGATTTCAACTCCACGACAGAGGAGGATCGTACCAAC
* * *
1459090 GGATCCATGATTTCAATTCCACGACGGAGGATATCGTGCACACACATCCACGGTTCAACTTCACG
196 GGATCCACGATTTCAACTCCACGACAGAGGA-ATCGTGCACACACATCCACGGTTCAACTTCACG
* * * **
1459155 ACGAAGGGAATCGTACACACAAGCAGTATCTATCTCTAGATTGGATTTCAACTTCACGTAGAATT
260 ACGAAGGGAATCGTACACACAAGCAGCATCCATCTCTAGATTGGATTTCAACTTCACGTAAAAGG
1459220 ATATCCAACT
325 ATATCCAACT
* * *
1459230 CAAAGAAAGAGTGTATGTCAATAAACTTTCCAGTTTCAGAGCCAATTTCATCTTCACGACGAATG
1 CAAAGAAAGAGTGTCTGTCAATAAACTTTCCAGTTTCAGAGCCAATTTCAACTTCACGACGAAGG
*
1459295 ATATTGGACTCGAAACAACACAAGCTTGGATTTCAAACTTCACGACGAAGGATATTCAAGTCAAG
66 ATATTGGACTCGAAACAGCACAAGCTTGGATTTC-AACTTCACGACGAAGGATATTCAAGTCAAG
* * *
1459360 GCTCAACTTCACGACGAATGGGCCATCCACGATTTCAACTCCATGACAGAGGA-TATCGTACC-A
130 GCTCAACTTCACGACGAAGGGGCCATCCACGATTTCAACTCCACGACAGAGGAGGATCGTACCAA
*
1459423 CGGATCCACGATTTCAACTCCACGACAGAGG-ATCGTGCCCACACATCCACGGTTTCAACTTCAC
195 CGGATCCACGATTTCAACTCCACGACAGAGGAATCGTGCACACACATCCACGG-TTCAACTTCAC
*
1459487 GACGAAGGGAATCGTACACACAAGTAGCATCCATCTCTAGA-TGGATTTCAACTTCACG-ACAAA
259 GACGAAGGGAATCGTACACACAAGCAGCATCCATCTCTAGATTGGATTTCAACTTCACGTA-AAA
*
1459550 GGATATCCTACT
323 GGATATCCAACT
* *
1459562 CAAAGAAGGAGTGTCTGTCAATAAACTTTCCAGTTTCAGAGCCAATTTCAACTTCACGGCGAAGG
1 CAAAGAAAGAGTGTCTGTCAATAAACTTTCCAGTTTCAGAGCCAATTTCAACTTCACGACGAAGG
* * * *
1459627 ATATTAGACTCGAAAC-GTACAAGCTTGGATTTCAACTTCACGATGAAGCATATTCAAGT
66 ATATTGGACTCGAAACAGCACAAGCTTGGATTTCAACTTCACGACGAAGGATATTCAAGT
1459686 TAAGCCTTCA
Statistics
Matches: 416, Mismatches: 36, Indels: 12
0.90 0.08 0.03
Matches are distributed among these distances:
330 24 0.06
331 16 0.04
332 123 0.30
333 49 0.12
334 46 0.11
335 81 0.19
336 77 0.19
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.24
Consensus pattern (334 bp):
CAAAGAAAGAGTGTCTGTCAATAAACTTTCCAGTTTCAGAGCCAATTTCAACTTCACGACGAAGG
ATATTGGACTCGAAACAGCACAAGCTTGGATTTCAACTTCACGACGAAGGATATTCAAGTCAAGG
CTCAACTTCACGACGAAGGGGCCATCCACGATTTCAACTCCACGACAGAGGAGGATCGTACCAAC
GGATCCACGATTTCAACTCCACGACAGAGGAATCGTGCACACACATCCACGGTTCAACTTCACGA
CGAAGGGAATCGTACACACAAGCAGCATCCATCTCTAGATTGGATTTCAACTTCACGTAAAAGGA
TATCCAACT
Found at i:1459769 original size:42 final size:42
Alignment explanation
Indices: 1459710--1459869 Score: 266
Period size: 42 Copynumber: 3.8 Consensus size: 42
1459700 AGTGAAACAA
1459710 GTCATCAGTAAGTCTTCCGAGCATGATGCTTAAATCCTTCGG
1 GTCATCAGTAAGTCTTCCGAGCATGATGCTTAAATCCTTCGG
*
1459752 GTCATCAGTAAGTCTTCCGAGCATAATGCTTAAATCCTTCGG
1 GTCATCAGTAAGTCTTCCGAGCATGATGCTTAAATCCTTCGG
*
1459794 ATCATCAGTAAGTCTTCCGAGCATGATGCTTAAATCCTTCGG
1 GTCATCAGTAAGTCTTCCGAGCATGATGCTTAAATCCTTCGG
* * * *
1459836 GTCATCTGTAAGCCTTTCGAGCATGATACTTAAA
1 GTCATCAGTAAGTCTTCCGAGCATGATGCTTAAA
1459870 ATTTTTGGGA
Statistics
Matches: 110, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 110 1.00
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.31
Consensus pattern (42 bp):
GTCATCAGTAAGTCTTCCGAGCATGATGCTTAAATCCTTCGG
Found at i:1460505 original size:215 final size:214
Alignment explanation
Indices: 1460100--1460662 Score: 746
Period size: 215 Copynumber: 2.6 Consensus size: 214
1460090 TGAAGCAAAT
* *
1460100 CCAGATATGATATTCCCTCAGAAGAAGCGGAACAGATCCCTCTTTTCCAAGATTTGATATTCCCT
1 CCAGATCTGATATTCCCTCAGAGGAAGCGGAACAGAT-CCTCTTTT-CAAGATTTGATATTCCC-
**
1460165 TCAGAGT-A-AATGGAACAAGTCTTGCCACGATTCAATGGATCAAACTCTCCCATATCTGATATT
63 T--GAGTGACAGCGGAACAAGTCTT-CC-CGATTCAATGGATC-AACTCTCCCATATCTGATATT
* * * *
1460228 CCCTCAGAGGAAGCGGAACAGGTCTCTTTCAAGATTTGATATTTCCTTAGTAACAGCGGAACAAG
123 CCCTCAAAGGAAGCGGAACAGCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGCGGAACAAG
*
1460293 TCTACTCTGATTCAA-GAATCAACTTTC
188 TCTACCCTGATTCAATGAATCAA-TTTC
*
1460320 CCAGATCTGATATTCCCTCAGAGGAAGTGGAA-ACGAT-CTCTTTTCAAGA-TTGATATTCCCTG
1 CCAGATCTGATATTCCCTCAGAGGAAGCGGAACA-GATCCTCTTTTCAAGATTTGATATTCCCTG
* * *
1460382 AGTGACAGCGGAACAAATATGTCCCGATTCAATGGATCAACTCTCCCATATCTGATATTCCCTTA
65 AGTGACAGCGGAACAAGTCT-TCCCGATTCAATGGATCAACTCTCCCATATCTGATATTCCCTCA
*
1460447 AAGGAAGCGGAACAGATCTCTCTTTCAAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTA
129 AAGGAAGCGGAACAG--CTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGCGGAACAAGTCTA
1460512 CCCTGATTCAATGAATCAATTTC
192 CCCTGATTCAATGAATCAATTTC
*
1460535 CCAGATCTGATATTCCCTCAGAGGAAACGGAACAGATCCATCTTTTTCAAGATTTGATATTCCCT
1 CCAGATCTGATATTCCCTCAGAGGAAGCGGAACAGATCC-TC-TTTTCAAGATTTGATATTCCCT
* * * *
1460600 GA-TGACAGCGGAACAAGTCTACCCTGATTCAATGAATCAACAAC-CCCAGATCTGATATTCCCT
64 GAGTGACAGCGGAACAAGTCTTCCC-GATTCAATGGATCAAC-TCTCCCATATCTGATATTCCCT
1460663 GAGTGACAGC
Statistics
Matches: 307, Mismatches: 22, Indels: 30
0.86 0.06 0.08
Matches are distributed among these distances:
213 44 0.14
214 15 0.05
215 104 0.34
216 21 0.07
217 10 0.03
218 65 0.21
219 16 0.05
220 32 0.10
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.28
Consensus pattern (214 bp):
CCAGATCTGATATTCCCTCAGAGGAAGCGGAACAGATCCTCTTTTCAAGATTTGATATTCCCTGA
GTGACAGCGGAACAAGTCTTCCCGATTCAATGGATCAACTCTCCCATATCTGATATTCCCTCAAA
GGAAGCGGAACAGCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGCGGAACAAGTCTACCCT
GATTCAATGAATCAATTTC
Found at i:1460520 original size:109 final size:109
Alignment explanation
Indices: 1460100--1460682 Score: 692
Period size: 109 Copynumber: 5.3 Consensus size: 109
1460090 TGAAGCAAAT
* * *
1460100 CCAGATATGATATTCCCTCAGAAGAAGCGGAACAGATCCCTCTTTTCCAAGATTTGATATTCCCT
1 CCAGATCTGATATTCCCTCAGAGGAAGCGGAACAGATCTCTC-TTT-CAAGATTTGATATTCCC-
** * *
1460165 TCAGAGT-A-AATGGAACAAGTCTTGCCAC-GATTCAATGGATCAAACTCTC
63 T--GAGTGACAGCGGAACAAGTC-TACC-CTGATTCAATGAATC-AACTCTC
* * * *
1460214 CCATATCTGATATTCCCTCAGAGGAAGCGGAACAG--GTCTCTTTCAAGATTTGATATTTCCTTA
1 CCAGATCTGATATTCCCTCAGAGGAAGCGGAACAGATCTCTCTTTCAAGATTTGATATTCCCTGA
* * *
1460277 GTAACAGCGGAACAAGTCTACTCTGATTCAA-GAATCAACTTTC
66 GTGACAGCGGAACAAGTCTACCCTGATTCAATGAATCAACTCTC
*
1460320 CCAGATCTGATATTCCCTCAGAGGAAGTGGAA-ACGATCTCT-TTTCAAGA-TTGATATTCCCTG
1 CCAGATCTGATATTCCCTCAGAGGAAGCGGAACA-GATCTCTCTTTCAAGATTTGATATTCCCTG
* * * *
1460382 AGTGACAGCGGAACAAATATGTCCC-GATTCAATGGATCAACTCTC
65 AGTGACAGCGGAACAAGTCT-ACCCTGATTCAATGAATCAACTCTC
* * *
1460427 CCATATCTGATATTCCCTTAAAGGAAGCGGAACAGATCTCTCTTTCAAGATTTGATATTCCCTGA
1 CCAGATCTGATATTCCCTCAGAGGAAGCGGAACAGATCTCTCTTTCAAGATTTGATATTCCCTGA
*
1460492 GTGACAGCGGAACAAGTCTACCCTGATTCAATGAATCAA-TTTC
66 GTGACAGCGGAACAAGTCTACCCTGATTCAATGAATCAACTCTC
* *
1460535 CCAGATCTGATATTCCCTCAGAGGAAACGGAACAGATCCATCTTTTTCAAGATTTGATATTCCCT
1 CCAGATCTGATATTCCCTCAGAGGAAGCGGAACAGAT-C-TCTCTTTCAAGATTTGATATTCCCT
*
1460600 GA-TGACAGCGGAACAAGTCTACCCTGATTCAATGAATCAACAAC-C
64 GAGTGACAGCGGAACAAGTCTACCCTGATTCAATGAATCAAC-TCTC
1460645 CCAGATCTGATATTCCCT--GAGTGACAGCGGAACAGATC
1 CCAGATCTGATATTCCCTCAGAG-GA-AGCGGAACAGATC
1460683 CCTCATCATA
Statistics
Matches: 409, Mismatches: 42, Indels: 41
0.83 0.09 0.08
Matches are distributed among these distances:
105 1 0.00
106 72 0.18
107 63 0.15
108 64 0.16
109 99 0.24
110 72 0.18
111 3 0.01
112 3 0.01
114 32 0.08
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (109 bp):
CCAGATCTGATATTCCCTCAGAGGAAGCGGAACAGATCTCTCTTTCAAGATTTGATATTCCCTGA
GTGACAGCGGAACAAGTCTACCCTGATTCAATGAATCAACTCTC
Found at i:1465483 original size:59 final size:59
Alignment explanation
Indices: 1465336--1465484 Score: 137
Period size: 59 Copynumber: 2.5 Consensus size: 59
1465326 TTAGTCATTA
* * * *
1465336 AACTTTTAAATATTAT-AATTTCATCCCTAAATTGTGACTATCATTCTAAAGTAGTCCTC
1 AACTTTTAAACATT-TCCATTTCATCCCAAAATTGTCACTATCATTCTAAAGTAGTCCTC
* * *
1465395 AACTTTTAAACATTTCGATTTCATCCCCAAAATATGTCA-T-TCATTCTAAATTGGTCC-C
1 AACTTTTAAACATTTCCATTTCAT-CCCAAAAT-TGTCACTATCATTCTAAAGTAGTCCTC
*
1465453 TAACATTTTGAACA-TTCCATTTTCATCCCAAA
1 -AAC-TTTTAAACATTTCCA-TTTCATCCCAAA
1465485 TTATAAGTAT
Statistics
Matches: 76, Mismatches: 8, Indels: 12
0.79 0.08 0.12
Matches are distributed among these distances:
58 2 0.03
59 48 0.63
60 22 0.29
61 4 0.05
ACGTcount: A:0.33, C:0.22, G:0.06, T:0.39
Consensus pattern (59 bp):
AACTTTTAAACATTTCCATTTCATCCCAAAATTGTCACTATCATTCTAAAGTAGTCCTC
Found at i:1465735 original size:60 final size:57
Alignment explanation
Indices: 1465609--1465770 Score: 175
Period size: 60 Copynumber: 2.8 Consensus size: 57
1465599 TTTGCATGCT
* ** * *
1465609 TTTACGGATGAAATTAAATATTC-AAAGTTTGGGGACCAATTTAGAAATAGTCATAG
1 TTTAGGGATGAAATTAAATATTCAAAAGTTTAAGGACTAATTTAGAAAGAGTCATAG
* *
1465665 TTTAGGGATGAAATTAAAATGTTCAAAAGTTTAACGACTAATTTAGAATGAGAGTCATAG
1 TTTAGGGATGAAATT-AAATATTCAAAAGTTTAAGGACTAATTTAGAA--AGAGTCATAG
* * *
1465725 TTT-GGAGATGAAATTGGAATCTTTAAAAGTTTAAGGACTAATTTAG
1 TTTAGG-GATGAAATT-AAATATTCAAAAGTTTAAGGACTAATTTAG
1465771 GGACATATGA
Statistics
Matches: 89, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
56 14 0.16
57 7 0.08
58 19 0.21
59 2 0.02
60 47 0.53
ACGTcount: A:0.40, C:0.07, G:0.20, T:0.33
Consensus pattern (57 bp):
TTTAGGGATGAAATTAAATATTCAAAAGTTTAAGGACTAATTTAGAAAGAGTCATAG
Found at i:1465802 original size:2 final size:2
Alignment explanation
Indices: 1465795--1465834 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1465785 ATTAACGTAA
1465795 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1465835 TACTTGGTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1466967 original size:2 final size:2
Alignment explanation
Indices: 1466960--1466996 Score: 65
Period size: 2 Copynumber: 18.0 Consensus size: 2
1466950 TTTAACCATA
1466960 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
1466997 TCTTTTCACA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 32 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1469796 original size:21 final size:21
Alignment explanation
Indices: 1469754--1469796 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1469744 AGAAATTAAG
* * *
1469754 ATTTTTTATAAATATAATAAT
1 ATTTTTAATAAATAAAAAAAT
*
1469775 ATTTTTAATAATTAAAAAAAT
1 ATTTTTAATAAATAAAAAAAT
1469796 A
1 A
1469797 AATTACAAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
ATTTTTAATAAATAAAAAAAT
Found at i:1475144 original size:2 final size:2
Alignment explanation
Indices: 1475073--1475124 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
1475063 GTAATAGGAT
1475073 TA TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA TA
1475115 TA TA TA TA TA
1 TA TA TA TA TA
1475125 ATTGGAGTTG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1477291 original size:18 final size:18
Alignment explanation
Indices: 1477270--1477304 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1477260 CTTTAACCGA
*
1477270 GTTTTTTATTATTATTTT
1 GTTTTTAATTATTATTTT
*
1477288 GTTTTTAATTGTTATTT
1 GTTTTTAATTATTATTT
1477305 CGAGACTAAT
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:0.17, C:0.00, G:0.09, T:0.74
Consensus pattern (18 bp):
GTTTTTAATTATTATTTT
Found at i:1483757 original size:7 final size:7
Alignment explanation
Indices: 1483693--1483767 Score: 53
Period size: 7 Copynumber: 10.3 Consensus size: 7
1483683 CCCGGTCCAA
1483693 CATTGAC
1 CATTGAC
*
1483700 CATTTGGC
1 CA-TTGAC
1483708 CATTGAC
1 CATTGAC
*
1483715 CGTTTGA-
1 C-ATTGAC
*
1483722 CATTGAT
1 CATTGAC
*
1483729 CGTTGAC
1 CATTGAC
*
1483736 CGTTTGAC
1 C-ATTGAC
1483744 CATTTGAC
1 CA-TTGAC
*
1483752 CATTGAT
1 CATTGAC
1483759 CATTGAC
1 CATTGAC
1483766 CA
1 CA
1483768 AAAAGTCAAA
Statistics
Matches: 53, Mismatches: 10, Indels: 10
0.73 0.14 0.14
Matches are distributed among these distances:
6 4 0.08
7 26 0.49
8 23 0.43
ACGTcount: A:0.23, C:0.24, G:0.19, T:0.35
Consensus pattern (7 bp):
CATTGAC
Found at i:1483758 original size:30 final size:29
Alignment explanation
Indices: 1483710--1483766 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 29
1483700 CATTTGGCCA
* *
1483710 TTGACCGTTTGACATTGATCGTTGACCGT
1 TTGACCATTTGACATTGATCATTGACCGT
1483739 TTGACCATTTGACCATTGATCATTGACC
1 TTGACCATTTGA-CATTGATCATTGACC
1483767 AAAAAGTCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 11 0.44
30 14 0.56
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.37
Consensus pattern (29 bp):
TTGACCATTTGACATTGATCATTGACCGT
Found at i:1484988 original size:21 final size:21
Alignment explanation
Indices: 1484964--1485014 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
1484954 TACGAGTTAA
*
1484964 ACTTTTATAGTTAATTATTTT
1 ACTTTTATAGTTAATTATCTT
1484985 ACTTTTATAGTTAATTATCTT
1 ACTTTTATAGTTAATTATCTT
1485006 ACTTTTATA
1 ACTTTTATA
1485015 AATGTTAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.29, C:0.08, G:0.04, T:0.59
Consensus pattern (21 bp):
ACTTTTATAGTTAATTATCTT
Found at i:1495005 original size:8 final size:8
Alignment explanation
Indices: 1494994--1495065 Score: 67
Period size: 8 Copynumber: 9.2 Consensus size: 8
1494984 TTGGTCAACT
1494994 GTCAAACG
1 GTCAAACG
*
1495002 GTCAAATG
1 GTCAAACG
* *
1495010 ATCAAACA
1 GTCAAACG
1495018 GTCAAACG
1 GTCAAACG
*
1495026 GTCAAACA
1 GTCAAACG
* *
1495034 ATCAAA-A
1 GTCAAACG
1495041 GTCAAACG
1 GTCAAACG
1495049 GTC-AACG
1 GTCAAACG
*
1495056 GACAAACG
1 GTCAAACG
1495064 GT
1 GT
1495066 TAACGTTGGA
Statistics
Matches: 50, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
7 12 0.24
8 38 0.76
ACGTcount: A:0.44, C:0.22, G:0.19, T:0.14
Consensus pattern (8 bp):
GTCAAACG
Found at i:1495006 original size:15 final size:15
Alignment explanation
Indices: 1494986--1495070 Score: 62
Period size: 15 Copynumber: 5.5 Consensus size: 15
1494976 TTGACTTTTT
*
1494986 GGTCAACTGTCAAAC
1 GGTCAACGGTCAAAC
* *
1495001 GGTCAAATGATCAAAC
1 GGTC-AACGGTCAAAC
*
1495017 AGTCAAACGGTCAAAC
1 GGTC-AACGGTCAAAC
** **
1495033 AATCAAAAGTCAAAC
1 GGTCAACGGTCAAAC
*
1495048 GGTCAACGGACAAAC
1 GGTCAACGGTCAAAC
*
1495063 GGTTAACG
1 GGTCAACG
1495071 TTGGACCGGG
Statistics
Matches: 54, Mismatches: 15, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
15 30 0.56
16 24 0.44
ACGTcount: A:0.42, C:0.22, G:0.20, T:0.15
Consensus pattern (15 bp):
GGTCAACGGTCAAAC
Found at i:1495016 original size:16 final size:15
Alignment explanation
Indices: 1494986--1495053 Score: 64
Period size: 16 Copynumber: 4.4 Consensus size: 15
1494976 TTGACTTTTT
*
1494986 GGTCAACTGTCAAAC
1 GGTCAAATGTCAAAC
1495001 GGTCAAATGATCAAAC
1 GGTCAAATG-TCAAAC
* *
1495017 AGTCAAACGGTCAAAC
1 GGTCAAA-TGTCAAAC
** *
1495033 AATCAAAAGTCAAAC
1 GGTCAAATGTCAAAC
1495048 GGTCAA
1 GGTCAA
1495054 CGGACAAACG
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
15 19 0.43
16 24 0.55
17 1 0.02
ACGTcount: A:0.44, C:0.22, G:0.18, T:0.16
Consensus pattern (15 bp):
GGTCAAATGTCAAAC
Found at i:1495021 original size:24 final size:23
Alignment explanation
Indices: 1494994--1495053 Score: 93
Period size: 24 Copynumber: 2.6 Consensus size: 23
1494984 TTGGTCAACT
**
1494994 GTCAAACGGTCAAATGATCAAACA
1 GTCAAACGGTCAAACAATCAAA-A
1495018 GTCAAACGGTCAAACAATCAAAA
1 GTCAAACGGTCAAACAATCAAAA
1495041 GTCAAACGGTCAA
1 GTCAAACGGTCAA
1495054 CGGACAAACG
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
23 14 0.41
24 20 0.59
ACGTcount: A:0.47, C:0.22, G:0.17, T:0.15
Consensus pattern (23 bp):
GTCAAACGGTCAAACAATCAAAA
Found at i:1497230 original size:8 final size:8
Alignment explanation
Indices: 1497206--1497265 Score: 61
Period size: 8 Copynumber: 7.8 Consensus size: 8
1497196 CGGTCCAACG
*
1497206 TTGATCGT
1 TTGACCGT
1497214 TTG-CCGT
1 TTGACCGT
1497221 TTGACCGT
1 TTGACCGT
*
1497229 TTAACCGT
1 TTGACCGT
*
1497237 TTGACTGT
1 TTGACCGT
*
1497245 TTGATCGT
1 TTGACCGT
*
1497253 TTTACCG-
1 TTGACCGT
1497260 TTGACC
1 TTGACC
1497266 AAAAAGTTAA
Statistics
Matches: 42, Mismatches: 9, Indels: 3
0.78 0.17 0.06
Matches are distributed among these distances:
7 11 0.26
8 31 0.74
ACGTcount: A:0.13, C:0.22, G:0.22, T:0.43
Consensus pattern (8 bp):
TTGACCGT
Found at i:1498401 original size:4 final size:4
Alignment explanation
Indices: 1498392--1499826 Score: 2835
Period size: 4 Copynumber: 360.0 Consensus size: 4
1498382 TGATGTTTTA
1498392 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1498440 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1498488 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1498536 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1498584 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1498632 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1498680 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1498728 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1498776 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1498824 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1498872 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1498920 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT AC-- ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1498966 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1499014 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1499062 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1499110 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1499158 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1499206 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1499254 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1499302 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT --AT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1499348 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1499396 ACAT ACAT ACAT ACAT AC-T ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1499443 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1499491 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1499539 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1499587 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1499635 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1499683 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1499731 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1499779 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1499827 GCATGGCTTA
Statistics
Matches: 1426, Mismatches: 0, Indels: 10
0.99 0.00 0.01
Matches are distributed among these distances:
2 4 0.00
3 3 0.00
4 1419 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ACAT
Found at i:1500736 original size:30 final size:30
Alignment explanation
Indices: 1500700--1500759 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
1500690 AAAAGCTCCC
*
1500700 CCTTTTTCATTATTGAAATTGAATTTTTCA
1 CCTTTTTCATTATTGAAATTGAATATTTCA
*
1500730 CCTTTTTCATTCTTGAAATTGAATATTTCA
1 CCTTTTTCATTATTGAAATTGAATATTTCA
1500760 AACCATATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.27, C:0.15, G:0.07, T:0.52
Consensus pattern (30 bp):
CCTTTTTCATTATTGAAATTGAATATTTCA
Found at i:1503813 original size:21 final size:21
Alignment explanation
Indices: 1503788--1503844 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
1503778 CATGATGAAC
1503788 AGTATCGATACTGATGTAAGT
1 AGTATCGATACTGATGTAAGT
*
1503809 AGTATCGATACTAATGTAAGT
1 AGTATCGATACTGATGTAAGT
*
1503830 AGCATCGATACTGAT
1 AGTATCGATACTGAT
1503845 ATGGGGTATC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.35, C:0.12, G:0.21, T:0.32
Consensus pattern (21 bp):
AGTATCGATACTGATGTAAGT
Done.