Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008296.1 Hibiscus syriacus cultivar Beakdansim tig00110963_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: 1205179
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 6 of 7
Found at i:947712 original size:26 final size:28
Alignment explanation
Indices: 947638--947698 Score: 97
Period size: 28 Copynumber: 2.2 Consensus size: 28
947628 CAAAACTTTG
*
947638 TTTCAAAAGAAATAGA-CTCAAAGATTTT
1 TTTCAAAAGAAACA-ATCTCAAAGATTTT
947666 TTTCAAAAGAAACAATCTCAAAGATTTT
1 TTTCAAAAGAAACAATCTCAAAGATTTT
947694 TTTCA
1 TTTCA
947699 CAAAATTGTC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
27 1 0.03
28 30 0.97
ACGTcount: A:0.44, C:0.13, G:0.08, T:0.34
Consensus pattern (28 bp):
TTTCAAAAGAAACAATCTCAAAGATTTT
Found at i:948029 original size:36 final size:36
Alignment explanation
Indices: 947945--948048 Score: 133
Period size: 36 Copynumber: 3.0 Consensus size: 36
947935 GAGAAAATGA
* *
947945 TGTCTCAAGCGAGACAAAATTTG-CTTTA-AGATAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAT
* **
947979 AGTCTCAAATGAGACAAAATTTGTTTTTAGAGAAAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAT
*
948015 TGTCTCAAGCGAGACAAAGTTTGTTTTT-GAGAAA
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAA
948049 ACGATCTCAA
Statistics
Matches: 59, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
34 20 0.34
35 10 0.17
36 29 0.49
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.33
Consensus pattern (36 bp):
TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAT
Found at i:948076 original size:36 final size:36
Alignment explanation
Indices: 947946--948064 Score: 120
Period size: 36 Copynumber: 3.4 Consensus size: 36
947936 AGAAAATGAT
* * *
947946 GTCTCAAGCGAGACAAAATTTG-CTTTA-AGATATA-
1 GTCTCAAGTGAGACAAAATTTGTTTTTAGAGA-AAAC
* **
947980 GTCTCAAATGAGACAAAATTTGTTTTTAGAGAAATT
1 GTCTCAAGTGAGACAAAATTTGTTTTTAGAGAAAAC
* *
948016 GTCTCAAGCGAGACAAAGTTTGTTTTT-GAGAAAAC
1 GTCTCAAGTGAGACAAAATTTGTTTTTAGAGAAAAC
948051 GATCTCAAGTGAGA
1 G-TCTCAAGTGAGA
948065 TCAACTTTGT
Statistics
Matches: 70, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
34 20 0.29
35 12 0.17
36 38 0.54
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (36 bp):
GTCTCAAGTGAGACAAAATTTGTTTTTAGAGAAAAC
Found at i:948195 original size:105 final size:105
Alignment explanation
Indices: 948016--948248 Score: 284
Period size: 105 Copynumber: 2.2 Consensus size: 105
948006 TAGAGAAATT
*
948016 GTCTCAAGCGAGAC-AAAGTTTGTTTTTG--AG-AA-AACGATCTCAA-GTGAGATCAACTTTGT
1 GTCTCAAGCGAGACGAAA-TTTG-TTTTGAAAGAAACAACAATCT-AAGGTGAGATCAACTTTGT
*
948075 TTAATGTGAAACAAATT-AGAAATTTGGATCTCAAAGGGAAAAG
63 TTAATGTGAAACAAATTCA-AAATTTGGATCTCAAAGGAAAAAG
* * *
948118 GTCTCAAGCGAGATGAAATTTGTTTTGAAAGAAACAACAATCTAAGGTGAGATTAATTTTGTTTT
1 GTCTCAAGCGAGACGAAATTTGTTTTGAAAGAAACAACAATCTAAGGTGAGATCAACTTTG-TTT
* * *
948183 AA-GTGAATCAAATTCAAAATTTGTATCTCAAAGGAAAAAT
65 AATGTGAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
*
948223 GTCTCAAGCGAGACGCAATTTGTTTT
1 GTCTCAAGCGAGACGAAATTTGTTTT
948249 AAAATTCTCA
Statistics
Matches: 113, Mismatches: 10, Indels: 13
0.83 0.07 0.10
Matches are distributed among these distances:
101 5 0.04
102 17 0.15
103 5 0.04
104 4 0.04
105 76 0.67
106 6 0.05
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.31
Consensus pattern (105 bp):
GTCTCAAGCGAGACGAAATTTGTTTTGAAAGAAACAACAATCTAAGGTGAGATCAACTTTGTTTA
ATGTGAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
Found at i:952558 original size:30 final size:31
Alignment explanation
Indices: 952500--952559 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
952490 ATGAAAAATG
*
952500 ACACAAACAAATGAGAAAAAATGAGTTAGTA
1 ACACAAACAAATGAGAAAAAACGAGTTAGTA
*
952531 ACACAAACAAAAT-AG-AGAAACGAGTTAGT
1 ACACAAAC-AAATGAGAAAAAACGAGTTAGT
952560 GCAAGCAAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 12 0.46
31 10 0.38
32 4 0.15
ACGTcount: A:0.57, C:0.12, G:0.17, T:0.15
Consensus pattern (31 bp):
ACACAAACAAATGAGAAAAAACGAGTTAGTA
Found at i:955841 original size:3 final size:3
Alignment explanation
Indices: 955833--955897 Score: 69
Period size: 3 Copynumber: 21.3 Consensus size: 3
955823 AAAATATGTA
* *
955833 AAT AAT AAT GAT AAT GAAT -AT AAT AAT AAT AAAT AAT AAT AAT AAA
1 AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT
* *
955879 AAT AAC GAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT A
955898 TATATAAAAA
Statistics
Matches: 51, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
2 2 0.04
3 43 0.84
4 6 0.12
ACGTcount: A:0.65, C:0.02, G:0.05, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:956737 original size:4 final size:4
Alignment explanation
Indices: 956728--956756 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
956718 CTATCCCCAA
956728 TCTT TCTT TCTT TCTT TCTT TCTT TCTT T
1 TCTT TCTT TCTT TCTT TCTT TCTT TCTT T
956757 TCTCTAGCCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TCTT
Found at i:966181 original size:31 final size:31
Alignment explanation
Indices: 966143--966217 Score: 141
Period size: 31 Copynumber: 2.4 Consensus size: 31
966133 AGAGTCAAGG
*
966143 GTTTACCTTTGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
966174 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
966205 GTTTACCTATGTT
1 GTTTACCTATGTT
966218 ATATGATATG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.17, C:0.19, G:0.21, T:0.43
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:968007 original size:31 final size:30
Alignment explanation
Indices: 967969--968093 Score: 146
Period size: 31 Copynumber: 4.0 Consensus size: 30
967959 AGAGTCAAGG
*
967969 GTTTACCTTTGTTCTTCGAGACATATGGACT
1 GTTTACCTATGTTCTTCG-GACATATGGACT
*
968000 GTTTACCTATGTTCTTCGGGACATATGAACT
1 GTTTACCTATGTTCTTC-GGACATATGGACT
*
968031 GTTTACCTATGTTTTTCGGAACATATGGACT
1 GTTTACCTATGTTCTTCGG-ACATATGGACT
*
968062 GATTACCTA-GATTCTTCGGGATC-TATGGACT
1 GTTTACCTATG-TTCTTC-GGA-CATATGGACT
968093 G
1 G
968094 GTCCTTCGGG
Statistics
Matches: 83, Mismatches: 6, Indels: 10
0.84 0.06 0.10
Matches are distributed among these distances:
30 3 0.04
31 76 0.92
32 4 0.05
ACGTcount: A:0.22, C:0.18, G:0.21, T:0.39
Consensus pattern (30 bp):
GTTTACCTATGTTCTTCGGACATATGGACT
Found at i:969830 original size:30 final size:30
Alignment explanation
Indices: 969796--969860 Score: 121
Period size: 30 Copynumber: 2.2 Consensus size: 30
969786 TTGCTACAGT
*
969796 GACCTCCATAGGTCTCCAGGAGTACACGAC
1 GACCTCCATAGGTCTCCAGGAGCACACGAC
969826 GACCTCCATAGGTCTCCAGGAGCACACGAC
1 GACCTCCATAGGTCTCCAGGAGCACACGAC
969856 GACCT
1 GACCT
969861 ACCTAGTGTG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.26, C:0.35, G:0.23, T:0.15
Consensus pattern (30 bp):
GACCTCCATAGGTCTCCAGGAGCACACGAC
Found at i:969979 original size:19 final size:19
Alignment explanation
Indices: 969955--969992 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
969945 TGTAACAAGG
* *
969955 AGCACTTGGCGACCTATGA
1 AGCACTTGACGACCAATGA
969974 AGCACTTGACGACCAATGA
1 AGCACTTGACGACCAATGA
969993 GGTGACTGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.26, G:0.24, T:0.18
Consensus pattern (19 bp):
AGCACTTGACGACCAATGA
Found at i:973046 original size:57 final size:57
Alignment explanation
Indices: 972958--973077 Score: 240
Period size: 57 Copynumber: 2.1 Consensus size: 57
972948 GATTAAAAAA
972958 ATTATTGTTTTATTGAGGTTCTAGGTTAGAGCAATTATATTTGTAGAGTATACACAC
1 ATTATTGTTTTATTGAGGTTCTAGGTTAGAGCAATTATATTTGTAGAGTATACACAC
973015 ATTATTGTTTTATTGAGGTTCTAGGTTAGAGCAATTATATTTGTAGAGTATACACAC
1 ATTATTGTTTTATTGAGGTTCTAGGTTAGAGCAATTATATTTGTAGAGTATACACAC
973072 ATTATT
1 ATTATT
973078 AATTAATAAA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 63 1.00
ACGTcount: A:0.30, C:0.08, G:0.18, T:0.43
Consensus pattern (57 bp):
ATTATTGTTTTATTGAGGTTCTAGGTTAGAGCAATTATATTTGTAGAGTATACACAC
Found at i:974481 original size:20 final size:20
Alignment explanation
Indices: 974458--974521 Score: 53
Period size: 19 Copynumber: 3.2 Consensus size: 20
974448 TAGCATTTAG
974458 ATAAAT-TTATTAATAATTTT
1 ATAAATATT-TTAATAATTTT
* *
974478 AT-AATCTTTTAATAAATTTA
1 ATAAATATTTTAAT-AATTTT
*
974498 ATAAGTATTTT-ATAATTTT
1 ATAAATATTTTAATAATTTT
*
974517 TTAAA
1 ATAAA
974522 CTTTATTGAC
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
19 16 0.46
20 13 0.37
21 6 0.17
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (20 bp):
ATAAATATTTTAATAATTTT
Found at i:974491 original size:19 final size:20
Alignment explanation
Indices: 974467--974516 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
974457 GATAAATTTA
*
974467 TTAATAATTTTATAA-TCTT
1 TTAATAATTTTATAAGTATT
*
974486 TTAATAAATTTAATAAGTATT
1 TTAAT-AATTTTATAAGTATT
974507 TT-ATAATTTT
1 TTAATAATTTT
974517 TTAAACTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 10 0.38
20 11 0.42
21 5 0.19
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (20 bp):
TTAATAATTTTATAAGTATT
Found at i:974512 original size:31 final size:30
Alignment explanation
Indices: 974434--974520 Score: 95
Period size: 31 Copynumber: 2.8 Consensus size: 30
974424 TTCGATAATA
* *
974434 TAATAATTATTTTAT-AGCATTTAGATAAATT
1 TAATAA-TATTTTATAATCTTTTA-ATAAATT
*
974465 TATTAATAATTTTATAATCTTTTAATAAATT
1 TAATAAT-ATTTTATAATCTTTTAATAAATT
*
974496 TAATAAGTATTTTATAATTTTTTAA
1 TAATAA-TATTTTATAATCTTTTAA
974521 ACTTTATTGA
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
30 1 0.02
31 40 0.83
32 7 0.15
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.53
Consensus pattern (30 bp):
TAATAATATTTTATAATCTTTTAATAAATT
Found at i:978394 original size:26 final size:23
Alignment explanation
Indices: 978370--978417 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
978360 ATAAAATATA
* *
978370 ATAACATACTAGGTAGCGCTTAT
1 ATAATATAATAGGTAGCGCTTAT
*
978393 ATAATGTAATAGGTAGCGCTTAT
1 ATAATATAATAGGTAGCGCTTAT
978416 AT
1 AT
978418 TTACATATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAATATAATAGGTAGCGCTTAT
Found at i:978866 original size:23 final size:23
Alignment explanation
Indices: 978831--978903 Score: 110
Period size: 23 Copynumber: 3.2 Consensus size: 23
978821 ATACTTTACA
* *
978831 ATATAACCACTACCTATTACATT
1 ATATAAACGCTACCTATTACATT
978854 ATATAAACGCTACCTATTACATT
1 ATATAAACGCTACCTATTACATT
* *
978877 ATATAAGCGCTACCTATTACATC
1 ATATAAACGCTACCTATTACATT
978900 ATAT
1 ATAT
978904 TTTTACCTAT
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:0.38, C:0.23, G:0.04, T:0.34
Consensus pattern (23 bp):
ATATAAACGCTACCTATTACATT
Found at i:979284 original size:430 final size:429
Alignment explanation
Indices: 978484--979965 Score: 2645
Period size: 430 Copynumber: 3.5 Consensus size: 429
978474 TATTACGTTA
** *
978484 TATTATATTGAAAGTGTTTATACTTTTTATAAAAATGATCGATACTTCTTTTAAAGTTACGTAAT
1 TATTATATTGAAAGTGTCCATACTTTTTATAAAAATGATCGATACTTCTTTTAAAGTTATGTAAT
978549 TTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCC-CCTTACAATATTAATTTAATAATTT
66 TTATGTTTCAA-TTTTTTTAATAGTGTTTCATGTTTTCCACC-TACAATATTAATTTAATAATTT
978613 CATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTAT-AAATAATATTTAGAATTTTTAA-T
129 CATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTTTAATT
978676 T--TAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATA
194 TAATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATA
978739 TCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACAC
259 TCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACAC
* *
978804 TTTTATAAAAATGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGCTACCT
324 TTTTATAAAAAGGATAGATACTTTACAATATAA-CACTACCTATTACATTATATAAACGATACCT
978869 ATTACATTATATAAGCGCTACCTATTACATCATATTTTTACC
388 ATTACATTATATAAGCGCTACCTATTACATCATATTTTTACC
*
978911 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
1 TATTATATTGAAAGTGTCCATACTTTTTATAAAAATGATCGATACTTCTTTTAAAGTTATGTAAT
*
978976 TTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCATCTACAATATTAATTTAATAATTTC
66 TTATGTTTCAA-TTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
*
979041 ATTTGCAC-AAAAATTATTTGATTATTTTGATATTTTATAAAATAATATTTAGAATTTTTAATTT
130 ATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTTTAATTT
*
979105 AATAATAATATATATCGTAACGTAAAAAATAAATCATTATACGCCTATAATTACTAAATTAATAT
195 AATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATAT
* **
979170 CTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCTACAGTGAAAAAAGTATAAACACT
260 CTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACT
*
979235 TTTATATAAAGGATAGATACTTTACAATATAATCACTACCTATTACATTATATAAACGATACCTA
325 TTTATAAAAAGGATAGATACTTTACAATATAA-CACTACCTATTACATTATATAAACGATACCTA
979300 TTACATTATATAAGCGCTACCTATTACATCATATTTTTACC
389 TTACATTATATAAGCGCTACCTATTACATCATATTTTTACC
* *
979341 TATTATATTGAAAGTGACCATACTATTTATAAAAATGATCGATACTTCTTTTAAAGTTATGTAAT
1 TATTATATTGAAAGTGTCCATACTTTTTATAAAAATGATCGATACTTCTTTTAAAGTTATGTAAT
979406 TTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCA
66 TTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCA
* * *
979471 TTTGCACAAAAATTTTTTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTA
131 TTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTTTAATTTA
*
979536 ATAATAATATATATCATAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATC
196 ATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATC
* *
979601 TTAAAACTCACTCAAAGGATAACCTTAAATTAATGTCTTCCACAGTGAAAAAAGTATGGACACTT
261 TTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTT
*
979666 TTATAAAAAGGATAGATACTTTACAATATAACAACTACCTATTACATTATATAAACGATATCTAT
326 TTATAAAAAGGATAGATACTTTACAATATAAC-ACTACCTATTACATTATATAAACGATACCTAT
979731 TACATTATATAAGCGCTACCTATTACATCATATTTTTACC
390 TACATTATATAAGCGCTACCTATTACATCATATTTTTACC
979771 TATTATATTGAAAGTGTCCATACTTTTTATAAAAATGATCGATACTTCTTTTAAAGTTATGTAAT
1 TATTATATTGAAAGTGTCCATACTTTTTATAAAAATGATCGATACTTCTTTTAAAGTTATGTAAT
*
979836 TTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCA
66 TTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCA
*
979901 TTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAA-TTTAAATTTA
131 TTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTTTAATTTA
979965 A
196 A
979966 CAACATTAAC
Statistics
Matches: 1010, Mismatches: 38, Indels: 12
0.95 0.04 0.01
Matches are distributed among these distances:
426 29 0.03
427 153 0.15
428 3 0.00
429 71 0.07
430 754 0.75
ACGTcount: A:0.39, C:0.12, G:0.07, T:0.42
Consensus pattern (429 bp):
TATTATATTGAAAGTGTCCATACTTTTTATAAAAATGATCGATACTTCTTTTAAAGTTATGTAAT
TTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCA
TTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTTTAATTTA
ATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATC
TTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTT
TTATAAAAAGGATAGATACTTTACAATATAACACTACCTATTACATTATATAAACGATACCTATT
ACATTATATAAGCGCTACCTATTACATCATATTTTTACC
Found at i:979287 original size:23 final size:23
Alignment explanation
Indices: 979261--979333 Score: 94
Period size: 23 Copynumber: 3.2 Consensus size: 23
979251 ATACTTTACA
*
979261 ATATAATCACTACCTATTACATT
1 ATATAAACACTACCTATTACATT
979284 ATATAAACGA-TACCTATTACATT
1 ATATAAAC-ACTACCTATTACATT
* * *
979307 ATATAAGCGCTACCTATTACATC
1 ATATAAACACTACCTATTACATT
979330 ATAT
1 ATAT
979334 TTTTACCTAT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
23 43 0.98
24 1 0.02
ACGTcount: A:0.40, C:0.21, G:0.04, T:0.36
Consensus pattern (23 bp):
ATATAAACACTACCTATTACATT
Found at i:979730 original size:23 final size:23
Alignment explanation
Indices: 979701--979763 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
979691 ATATAACAAC
979701 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* * *
979724 TATCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
979747 TACCTATTACATCATAT
1 TACCTATTACATTATAT
979764 TTTTACCTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.38, C:0.19, G:0.05, T:0.38
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:980238 original size:39 final size:39
Alignment explanation
Indices: 980184--980270 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
980174 TCAAGTTGTA
*
980184 GATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
*
980223 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
980262 GATTTTGAT
1 GATTTTGAT
980271 GAGCATCGGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.17, C:0.14, G:0.21, T:0.48
Consensus pattern (39 bp):
GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
Found at i:980565 original size:18 final size:18
Alignment explanation
Indices: 980542--980578 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
980532 CGAAATATAT
980542 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
980560 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
980578 A
1 A
980579 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:980996 original size:25 final size:25
Alignment explanation
Indices: 980962--981011 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
980952 ATTATTTTTC
*
980962 CAAAGAATGTACCCATAACAATGTT
1 CAAAGAATGTACCCACAACAATGTT
*
980987 CAAATAATGTACCCACAACAATGTT
1 CAAAGAATGTACCCACAACAATGTT
981012 TAATTGATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.44, C:0.22, G:0.10, T:0.24
Consensus pattern (25 bp):
CAAAGAATGTACCCACAACAATGTT
Found at i:981313 original size:23 final size:23
Alignment explanation
Indices: 981287--981349 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
981277 ATATAACCAC
981287 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
981310 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
981333 TACCTATTACATCATAT
1 TACCTATTACATTATAT
981350 TTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:981747 original size:25 final size:25
Alignment explanation
Indices: 981690--981755 Score: 78
Period size: 25 Copynumber: 2.6 Consensus size: 25
981680 CACTCAAAAG
*
981690 ATGTATATACCTAAATATGTAGTTA
1 ATGTACATACCTAAATATGTAGTTA
*** *
981715 ACAAACATATCTAAATATGTAGTTA
1 ATGTACATACCTAAATATGTAGTTA
*
981740 TTGTACATACCTAAAT
1 ATGTACATACCTAAAT
981756 TTAATGATAA
Statistics
Matches: 31, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.42, C:0.12, G:0.09, T:0.36
Consensus pattern (25 bp):
ATGTACATACCTAAATATGTAGTTA
Found at i:984566 original size:183 final size:183
Alignment explanation
Indices: 984226--984566 Score: 560
Period size: 183 Copynumber: 1.9 Consensus size: 183
984216 TAAAATTACT
*
984226 GACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAATA
1 GACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAATA
* * * *
984291 TTAGAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGTTA
66 TTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCAGTATATTTATACCGGATA
* *
984356 TATTACCAAATTATCTATTACATTATAAATATGGGTTCCGATGTGTAAATGTC
131 CATTACCAAATTACCTATTACATTATAAATATGGGTTCCGATGTGTAAATGTC
984409 GACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAATA
1 GACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAATA
984474 TTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCAGTATATTTATACC-GATA
66 TTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCAGTATATTTATACCGGATA
* **
984538 GCATT-GCAAATTTACCTATTTTATTATAA
131 -CATTACCAAA-TTACCTATTACATTATAA
984567 TGTTGAAAGT
Statistics
Matches: 146, Mismatches: 10, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
182 7 0.05
183 139 0.95
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.35
Consensus pattern (183 bp):
GACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAATA
TTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCAGTATATTTATACCGGATA
CATTACCAAATTACCTATTACATTATAAATATGGGTTCCGATGTGTAAATGTC
Found at i:984974 original size:23 final size:23
Alignment explanation
Indices: 984911--984983 Score: 74
Period size: 23 Copynumber: 3.2 Consensus size: 23
984901 ATAGTTTACA
* *
984911 ATATAACCACTACCTATTACATT
1 ATATAAACGCTACCTATTACATT
* ** *
984934 ATATAAACGATATTTATTATATT
1 ATATAAACGCTACCTATTACATT
* *
984957 ATATAAGCGCTACCTATTACATC
1 ATATAAACGCTACCTATTACATT
984980 ATAT
1 ATAT
984984 TTTTACCTAT
Statistics
Matches: 38, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.40, C:0.18, G:0.04, T:0.38
Consensus pattern (23 bp):
ATATAAACGCTACCTATTACATT
Found at i:985363 original size:431 final size:431
Alignment explanation
Indices: 984569--985617 Score: 1903
Period size: 431 Copynumber: 2.4 Consensus size: 431
984559 TATTATAATG
984569 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATAC-TTTTTTAAAGATATGTAA-TTATGTT
1 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGATATGTAATTTATGTT
984632 TCAATTTTTTTTAAGTATGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
66 TCAATTTTTTTTAAGTATGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
*
984697 CAAAAAATTATTTGATTATTTTGATATTTTATAAAATAATATTTAGAATTTTTAATTTAATAATA
131 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTTTAATTTAATAATA
984762 ATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAA
196 ATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAA
* *
984827 CTCACTCAAAAGATAACCTTAAATTAATGTTTTCCATAGTGAAAAAAGTATAGACACTTTTATAA
261 CTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATAGACAATTTTATAA
* * ** *
984892 AAAGGATAGATAGTTTACAATATAACCACTACCTATTACATTATATAAACGATATTTATTATATT
326 AAAGGATAGATACTTTACAATATAACAACTACCTATTACATTATATAAACGATACCTATTACATT
984957 ATATAAGCGCTACCTATTACATCATATTTTTACCTATTATA
391 ATATAAGCGCTACCTATTACATCATATTTTTACCTATTATA
984998 TTGAAAGTGTCCATACTTTTTATAAAAAAGGATCGATACTTTTTTTAAAGATATGTAATTTATGT
1 TTGAAAGTGTCCATACTTTTTAT-AAAAAGGATCGATACTTTTTTTAAAGATATGTAATTTATGT
*
985063 TTCAATTTTTTTTAAGTATGTTTCATGTTTTTCACCTACAATATTAATTTAATAATTTCATTTGC
65 TTCAATTTTTTTTAAGTATGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGC
985128 AC-AAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTTTAATTTAATAAT
130 ACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTTTAATTTAATAAT
985192 AATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAA
195 AATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAA
*
985257 ACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATATACAATTTTATA
260 ACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATAGACAATTTTATA
985322 AAAAGGATAGATACTTTACAATATAACAACTACCTATTACATTATATAAACGATACCTATTACAT
325 AAAAGGATAGATACTTTACAATATAACAACTACCTATTACATTATATAAACGATACCTATTACAT
985387 TATATAAGCGCTACCTATTACATCATATTTTTACCTATTATA
390 TATATAAGCGCTACCTATTACATCATATTTTTACCTATTATA
*
985429 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAAGTTATGTAATTTATGT
1 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTT-AAAGATATGTAATTTATGT
* *
985494 TTCAA-TTTTTTTAA-TAGTGTTTTATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTA
65 TTCAATTTTTTTTAAGTA-TGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTG
*
985557 CACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAA-TTTAAATTTAA
129 CACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTTTAATTTAA
985618 CAACATTAAC
Statistics
Matches: 599, Mismatches: 15, Indels: 11
0.96 0.02 0.02
Matches are distributed among these distances:
429 25 0.04
430 102 0.17
431 400 0.67
432 72 0.12
ACGTcount: A:0.39, C:0.11, G:0.08, T:0.42
Consensus pattern (431 bp):
TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGATATGTAATTTATGTT
TCAATTTTTTTTAAGTATGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTTTAATTTAATAATA
ATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAA
CTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATAGACAATTTTATAA
AAAGGATAGATACTTTACAATATAACAACTACCTATTACATTATATAAACGATACCTATTACATT
ATATAAGCGCTACCTATTACATCATATTTTTACCTATTATA
Found at i:985378 original size:23 final size:23
Alignment explanation
Indices: 985352--985414 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
985342 ATATAACAAC
985352 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
985375 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
985398 TACCTATTACATCATAT
1 TACCTATTACATTATAT
985415 TTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:987008 original size:3 final size:3
Alignment explanation
Indices: 987000--987044 Score: 63
Period size: 3 Copynumber: 15.0 Consensus size: 3
986990 ACTTGTTTGG
* * *
987000 ATC ATC ATC TTC ATC ATC ATC ATC ATC ATC GTC ATC ATC TTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
987045 GCCAGCTTCA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.27, C:0.33, G:0.02, T:0.38
Consensus pattern (3 bp):
ATC
Found at i:987017 original size:12 final size:12
Alignment explanation
Indices: 987004--987092 Score: 79
Period size: 12 Copynumber: 7.4 Consensus size: 12
986994 GTTTGGATCA
* *
987004 TCATCTTCATCA
1 TCATCGTCATCT
* *
987016 TCATCATCATCA
1 TCATCGTCATCT
* *
987028 TCGTCATCATCT
1 TCATCGTCATCT
* *
987040 TCATCGCCAGCT
1 TCATCGTCATCT
* *
987052 TCATTGTCATCA
1 TCATCGTCATCT
987064 TCATCGTCATCT
1 TCATCGTCATCT
*
987076 TCATCGTCAGCT
1 TCATCGTCATCT
987088 TCATC
1 TCATC
987093 TTCTGCGACC
Statistics
Matches: 63, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 63 1.00
ACGTcount: A:0.21, C:0.34, G:0.08, T:0.37
Consensus pattern (12 bp):
TCATCGTCATCT
Found at i:987023 original size:18 final size:18
Alignment explanation
Indices: 987004--987095 Score: 69
Period size: 18 Copynumber: 5.1 Consensus size: 18
986994 GTTTGGATCA
* *
987004 TCATCTTCATCATCATCA
1 TCATCATCATCATCATCT
*
987022 TCATCATCGTCATCATCT
1 TCATCATCATCATCATCT
** * *
987040 TCATCGCCAGCTTCAT-T
1 TCATCATCATCATCATCT
*
987057 GTCATCATCATCGTCATCT
1 -TCATCATCATCATCATCT
* * *
987076 TCATCGTCAGCTTCATCT
1 TCATCATCATCATCATCT
987094 TC
1 TC
987096 TGCGACCGCT
Statistics
Matches: 57, Mismatches: 15, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
17 1 0.02
18 55 0.96
19 1 0.02
ACGTcount: A:0.21, C:0.34, G:0.08, T:0.38
Consensus pattern (18 bp):
TCATCATCATCATCATCT
Found at i:987062 original size:36 final size:36
Alignment explanation
Indices: 987022--987091 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
987012 ATCATCATCA
*
987022 TCATCATCGTCATCATCTTCATCGCCAGCTTCATTG
1 TCATCATCATCATCATCTTCATCGCCAGCTTCATTG
* *
987058 TCATCATCATCGTCATCTTCATCGTCAGCTTCAT
1 TCATCATCATCATCATCTTCATCGCCAGCTTCAT
987092 CTTCTGCGAC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.20, C:0.33, G:0.10, T:0.37
Consensus pattern (36 bp):
TCATCATCATCATCATCTTCATCGCCAGCTTCATTG
Found at i:987095 original size:6 final size:6
Alignment explanation
Indices: 987004--987095 Score: 60
Period size: 6 Copynumber: 15.3 Consensus size: 6
986994 GTTTGGATCA
* * * * * * * *
987004 TCATCT TCATCA TCATCA TCATCA TCGTCA TCATCT TCATCG CCAGCT
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT
* * * *
987052 TCAT-T GTCATCA TCATCG TCATCT TCATCG TCAGCT TCATCT TC
1 TCATCT -TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TC
987096 TGCGACCGCT
Statistics
Matches: 67, Mismatches: 17, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
5 1 0.01
6 66 0.99
ACGTcount: A:0.21, C:0.34, G:0.08, T:0.38
Consensus pattern (6 bp):
TCATCT
Found at i:988869 original size:190 final size:194
Alignment explanation
Indices: 988542--989796 Score: 1916
Period size: 195 Copynumber: 6.6 Consensus size: 194
988532 TTTAAATTAG
*
988542 TATCGACAC-AACTAAAAAGTGTCGACACATTATTTAGACATA-TCTCTCATAAAACC-ATATAC
1 TATCGACACAAACTAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAC
988604 TTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTT-GGTTCGATG-TTTTGGGATC
66 TTGTACCGGTTAGATTGAAAAATTACATATTACA-TAT--TTTTGGGTTCGATGTTTTTGGGATC
*
988667 GACACCTTTTATATATGGATCGACACTTTATGG-TGCACCCTGTTTTCCATTCATTCTGGACCAA
128 GACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCAA
988731 AA
193 AA
*
988733 TATCGACAC-CACT-AAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA-AC
1 TATCGACACAAACTAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAC
988795 TTGTACCGGTTAGATTG-AAAATTACATATTACTATATTTTTGGGTTCGATGTTTTTGGGATCGA
66 TTGTACCGGTTAGATTGAAAAATTACATATTAC-ATATTTTTGGGTTCGATGTTTTTGGGATCGA
*
988859 CACTTTTTATATATGGATCGACACTTTATGGTTGCACCTTG-TTTCCATTCATTCTGGACCAAAA
130 CACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCAAAA
* *
988923 AATCGACACCAACTAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAC
1 TATCGACACAAACTAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAC
988988 TTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTT-GGATC
66 TTGTACCGGTTAGATTGAAAAATTACATATTACA-TAT--TTTTGGGTTCGATGTTTTTGGGATC
*
989052 GAAACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCAA
128 GACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACC-A
989117 AAA
192 AAA
*
989120 TATCAACACAAACTAAAAAGTGTCGACACATTATTTAGAC-TATTCTCTCATAAAACCGGTATAC
1 TATCGACACAAACTAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAC
*
989184 TTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTGGGTTCGATGTTTTTGGGATCG
66 TTGTACCGGTTAGATTGAAAAATTACATATTACA-TAT-TTTTGGGTTCGATGTTTTTGGGATCG
* *
989249 ACACTTTTTATATATGGATCGACACTTTAATGGTTGCACCATGTTTTCCATTCATTCTGGAACAA
129 ACACTTTTTATATATGGATCGACACTTT-ATGGTTGCACCCTGTTTTCCATTCATTCTGGACCAA
989314 AA
193 AA
989316 -ATCGACACAAACTAAAATA-TGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAA-AGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
*
989379 CTTGTA-CGGTTAGATTGAAAAATTACATATTACATTATACTTTGGGTTCGATGTTTTTGGGATC
65 CTTGTACCGGTTAGATTGAAAAATTACATATTACA-TAT-TTTTGGGTTCGATGTTTTTGGGATC
* *
989443 GACACTTTTT-TATATGGAT-----C-----GGTTGCACCATGTTTTCCATTCATTCTGGAACAA
128 GACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGG-ACCA
989497 AAA
192 AAA
989500 TATCGACACAAACTAAAATAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACC-GTATA
1 TATCGACACAAACTAAAA-AGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
989564 CTTGTACCGGTTAGATTG-AAAATTACATATTACATTACTTTTT-GGTTCGA--TTTTTGGGATC
65 CTTGTACCGGTTAGATTGAAAAATTACATATTACA-TA-TTTTTGGGTTCGATGTTTTTGGGATC
*
989625 GACACTTTTTATATATGGATCGACAC-TTATGGTTGCACCCTGTTTTCCATTCATTCTGGAACAA
128 GACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGG-ACCA
989689 AAA
192 AAA
*
989692 TATCGACACAAACT-AAAAGTGTCGACATATTATTTAGACATATTCTCTC-TAAAACC-GTATAC
1 TATCGACACAAACTAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAC
* * *
989754 TTGTACCGGTTAGATTGAAAATTTATATATTACATATTGTTGG
66 TTGTACCGGTTAGATTGAAAAATTACATATTACATATTTTTGG
989797 CCATATTGTA
Statistics
Matches: 1003, Mismatches: 25, Indels: 74
0.91 0.02 0.07
Matches are distributed among these distances:
182 21 0.02
183 38 0.04
184 12 0.01
185 52 0.05
186 50 0.05
188 9 0.01
189 43 0.04
190 164 0.16
191 60 0.06
192 99 0.10
193 20 0.02
194 27 0.03
195 168 0.17
196 167 0.17
197 73 0.07
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.36
Consensus pattern (194 bp):
TATCGACACAAACTAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAC
TTGTACCGGTTAGATTGAAAAATTACATATTACATATTTTTGGGTTCGATGTTTTTGGGATCGAC
ACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCAAAA
Found at i:989166 original size:196 final size:198
Alignment explanation
Indices: 988542--989788 Score: 2006
Period size: 196 Copynumber: 6.5 Consensus size: 198
988532 TTTAAATTAG
*
988542 TATCGACAC-AACTAAAAAGTGTCGACACATTATTTAGACATA-TCTCTCATAAAACC-ATATAC
1 TATCGACACAAACTAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAC
988604 TTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTT-GGTTCGATG-TTTTGGGATC
66 TTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGATC
* *
988667 GACACCTTTTATATATGGATCGACACTTTATGG-TGCACCCTGTTTTCCATTCATTCTGG-ACCA
131 GACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAACAA
988730 AAA
196 AAA
*
988733 TATCGACAC-CACT-AAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA-AC
1 TATCGACACAAACTAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAC
*
988795 TTGTACCGGTTAGATTG-AAAATTACATATTAC--TATATTTTTGGGTTCGATGTTTTTGGGATC
66 TTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGATC
* *
988857 GACACTTTTTATATATGGATCGACACTTTATGGTTGCACCTTG-TTTCCATTCATTCTGGACCAA
131 GACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAACAA
988921 AAA
196 AAA
*
988924 -ATCGACACCAACTAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAC
1 TATCGACACAAACTAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAC
988988 TTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTT-GGATC
66 TTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGATC
* *
989052 GAAACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCAA
131 GACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAACAA
989117 AAA
196 AAA
*
989120 TATCAACACAAACTAAAAAGTGTCGACACATTATTTAGAC-TATTCTCTCATAAAACCGGTATAC
1 TATCGACACAAACTAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAC
989184 TTGTACCGGTTAGATTGAAAAATTACATATTACATTATAC-TTTGGGTTCGATGTTTTTGGGATC
66 TTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGATC
*
989248 GACACTTTTTATATATGGATCGACACTTTAATGGTTGCACCATGTTTTCCATTCATTCTGGAAC-
131 GACACTTTTTATATATGGATCGACACTTT-ATGGTTGCACCCTGTTTTCCATTCATTCTGGAACA
989312 AAAA
195 AAAA
989316 -ATCGACACAAACTAAAATA-TGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAA-AGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
989379 CTTGTA-CGGTTAGATTGAAAAATTACATATTACATTATAC-TTTGGGTTCGATGTTTTTGGGAT
65 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGAT
*
989442 CGACACTTTTT-TATATGGAT-----C-----GGTTGCACCATGTTTTCCATTCATTCTGGAACA
130 CGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAACA
989496 AAAA
195 AAAA
989500 TATCGACACAAACTAAAATAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACC-GTATA
1 TATCGACACAAACTAAAA-AGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
*
989564 CTTGTACCGGTTAGATTG-AAAATTACATATTACA-T-TACTTTTTGGTTCGA--TTTTTGGGAT
65 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGAT
989624 CGACACTTTTTATATATGGATCGACAC-TTATGGTTGCACCCTGTTTTCCATTCATTCTGGAACA
130 CGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAACA
989688 AAAA
195 AAAA
*
989692 TATCGACACAAACT-AAAAGTGTCGACATATTATTTAGACATATTCTCTC-TAAAACC-GTATAC
1 TATCGACACAAACTAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAC
* *
989754 TTGTACCGGTTAGATTGAAAATTTATATATTACAT
66 TTGTACCGGTTAGATTGAAAAATTACATATTACAT
989789 ATTGTTGGCC
Statistics
Matches: 999, Mismatches: 22, Indels: 70
0.92 0.02 0.06
Matches are distributed among these distances:
182 21 0.02
183 44 0.04
184 15 0.02
185 46 0.05
186 49 0.05
188 9 0.01
189 40 0.04
190 154 0.15
191 64 0.06
192 99 0.10
193 19 0.02
194 24 0.02
195 168 0.17
196 178 0.18
197 69 0.07
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.36
Consensus pattern (198 bp):
TATCGACACAAACTAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAC
TTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGATC
GACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAACAA
AAA
Found at i:989951 original size:19 final size:18
Alignment explanation
Indices: 989912--989959 Score: 69
Period size: 19 Copynumber: 2.6 Consensus size: 18
989902 TTATATTCAC
*
989912 ATACAAAAATATAATCGT
1 ATACAAAATTATAATCGT
*
989930 ATACAAAATTATAAATCTT
1 ATACAAAATTAT-AATCGT
989949 ATACAAAATTA
1 ATACAAAATTA
989960 ACCCTACATT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 11 0.41
19 16 0.59
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.31
Consensus pattern (18 bp):
ATACAAAATTATAATCGT
Found at i:991757 original size:32 final size:31
Alignment explanation
Indices: 991715--991774 Score: 84
Period size: 32 Copynumber: 1.9 Consensus size: 31
991705 TTAATATCAC
*
991715 CCCTTAACACCCCAACTTCTTTCACCACTTCA
1 CCCTCAACACCCCAACTTCTTT-ACCACTTCA
* *
991747 CCCTCAACACCTCTACTTCTTTACCACT
1 CCCTCAACACCCCAACTTCTTTACCACT
991775 CCATCTATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 6 0.24
32 19 0.76
ACGTcount: A:0.23, C:0.47, G:0.00, T:0.30
Consensus pattern (31 bp):
CCCTCAACACCCCAACTTCTTTACCACTTCA
Found at i:991833 original size:21 final size:21
Alignment explanation
Indices: 991808--991851 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
991798 CCCCTTATGC
991808 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTGTATCTTCGACT
* *
991829 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTGTATCTTCGACT
991850 CT
1 CT
991852 TGATTGTCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.32, G:0.11, T:0.41
Consensus pattern (21 bp):
CTCTCAAGTGTATCTTCGACT
Found at i:994089 original size:20 final size:19
Alignment explanation
Indices: 994043--994089 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
994033 TCCGGTATCA
*
994043 TTTTACCGGTTTTATCATT
1 TTTTACCGATTTTATCATT
*
994062 TTGATACCGATTTTATCATAT
1 TT-TTACCGATTTTATCAT-T
994083 TTTTACC
1 TTTTACC
994090 TGTTATATCG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.21, C:0.17, G:0.09, T:0.53
Consensus pattern (19 bp):
TTTTACCGATTTTATCATT
Found at i:994496 original size:182 final size:178
Alignment explanation
Indices: 994010--994483 Score: 662
Period size: 180 Copynumber: 2.6 Consensus size: 178
994000 CGTATTTACG
*
994010 AAAGTATCGACACTTTCAATATATCCGGTAT-CATTTTACCGGTTTTATCATTTTGATACCGATT
1 AAAGTATCGACACTTTCAATATATCCGGTATGC--TTTACCGGTTTTATCATTTT-ATACCGGTT
* *
994074 TTATCATATTTTTACCTGTTATATCGTTGTGGATCGATATTTTTTTTAAAGTATCGACACATTAT
63 TTATCATATTTTTACCTGTTATATCGTTTTGGATCGATATATTTTTTAAAGTATCGACACATTAT
*
994139 AGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
128 AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
* * *
994190 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGTAACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGT-ATGCTTTACCGGTTTTATCATTTTAT-ACCGGTTT
* * * * *
994255 CATCATATTTTTACCTGGTATATCGTTTTGAATCGATACATTTTTTAAAAGTATCGACACTTTAT
64 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATATATTTTTT-AAAGTATCGACACATTAT
** *
994320 AGGATTTAAAACTGCTTCTCTTTTAAATTCACGAAGTGTCGATCCTTATATT
128 AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-T
* * *
994372 AAAGTACCGACACTTTAAATGTATCCGGTAGTGCTTTACCGGTTTTATCATTTCTATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTA-TGCTTTACCGGTTTTATCATTT-TATACCGGTTT
* * * *
994437 TGTCATAGTTTTACATGTTATATCGTTTTGGATCGACATATTTTTTA
64 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATATATTTTTTA
994484 TTTGGATCGA
Statistics
Matches: 258, Mismatches: 29, Indels: 13
0.86 0.10 0.04
Matches are distributed among these distances:
179 1 0.00
180 96 0.37
181 66 0.26
182 93 0.36
183 2 0.01
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.42
Consensus pattern (178 bp):
AAAGTATCGACACTTTCAATATATCCGGTATGCTTTACCGGTTTTATCATTTTATACCGGTTTTA
TCATATTTTTACCTGTTATATCGTTTTGGATCGATATATTTTTTAAAGTATCGACACATTATAGG
AGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
Found at i:995005 original size:228 final size:227
Alignment explanation
Indices: 994553--995027 Score: 819
Period size: 228 Copynumber: 2.1 Consensus size: 227
994543 CTTTTATACT
994553 TATGGACACTTTTATAAAAATGATATATACTTTTTTTAAAGTTATGTAATTTATATTTCAATTTT
1 TATGGACACTTTTATAAAAATGATATATACTTTTTTTAAAGTTATGTAATTTATATTTCAATTTT
994618 TTAATAGTGTTTCATGTTTTCAACCTACAATATTAATTTAATAATTTCATTTACACAAAAAATTA
66 TTAATAGTGTTTCATGTTTTCAACCTACAATATTAATTTAATAATTTCATTTACACAAAAAATTA
* *
994683 TTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAATAT
131 TTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACAAAAGAT
* *
994748 AATAATAAATATGTTTTCTACAATGAAATAAG
196 AATAATAAATATATTTTCTACAATGAAATAAA
* *
994780 TATGAACACTTTTATAAAAATGATATATA-TATTTTTTAAAGTTATGTAATTTATGTTTCAATTT
1 TATGGACACTTTTATAAAAATGATATATACT-TTTTTTAAAGTTATGTAATTTATATTTCAA-TT
* *
994844 TTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACACAAAAT
64 TTTTAATAGTGTTTCATGTTTTCAACCTACAATATTAATTTAATAATTTCATTTACACAAAAAAT
*
994909 TATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACAAAA
129 TATTTGATT-ATTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACAAAA
*
994974 GATAATAATAAATATATTTTC-ACAGTGAAATAAA
193 GATAATAATAAATATATTTTCTACAATGAAATAAA
995008 TATGGACACTTTTATAAAAA
1 TATGGACACTTTTATAAAAA
995028 GGGAAGATAC
Statistics
Matches: 234, Mismatches: 11, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
226 1 0.00
227 57 0.24
228 104 0.44
229 72 0.31
ACGTcount: A:0.41, C:0.08, G:0.07, T:0.45
Consensus pattern (227 bp):
TATGGACACTTTTATAAAAATGATATATACTTTTTTTAAAGTTATGTAATTTATATTTCAATTTT
TTAATAGTGTTTCATGTTTTCAACCTACAATATTAATTTAATAATTTCATTTACACAAAAAATTA
TTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACAAAAGAT
AATAATAAATATATTTTCTACAATGAAATAAA
Found at i:998128 original size:200 final size:197
Alignment explanation
Indices: 997706--998177 Score: 560
Period size: 200 Copynumber: 2.4 Consensus size: 197
997696 TTATATTATA
*
997706 AAAT-TACCTATTACATTATAATTATGAGTTTTGATGTTTTTGGGATCGATACTTTTTAAAAATG
1 AAATGTACCTATTACATTATAATTATG-GTTTCGATGTTTTTGGGATCGATAC-TTTTAAAAATG
* *
997770 TATCGACACTTTATGAGTGCACCCGTCTGGCATTCATTATGGACAAAATATATCGACACAAATTT
64 TATCGACACTTTATGAGTACACCCGTCTGGCATTCATTATGGACAAAATATATCGACACAAATTA
* * *
997835 AATAAGAATCGATACTTTATGATGACCTATTTTCTCATAAAACCGGTATATTTATACCAGTTACA
129 AACAAGAATCGATACATTATGATGACCTATTTTCTAATAAAACCGGTATATTTATACCAGTTACA
997900 TTGT
194 TTGT
* * * * *
997904 AAATTTACATATTGCATTATAATTATCGGTTTCGAT-TTTATTGGGATCAATACTTTTAATAATT
1 AAATGTACCTATTACATTATAATTAT-GGTTTCGATGTTT-TTGGGATCGATACTTTTAA-AAAT
* * * * * *
997968 GTATCGACACTTTATGCGTACACCCCGTTTGGGCATTTATTCTGGACAATAA-GTATCGACATAA
63 GTATCGACACTTTATGAGTACA-CCCGTCT-GGCATTCATTATGGACAA-AATATATCGACACAA
** * * * * *
998032 ATTAAACAAGTGTCGATACATTATGTTTACCTGTTTTCTAAT-TAACCGGTATATTTATATC-GA
125 ATTAAACAAGAATCGATACATTATGATGACCTATTTTCTAATAAAACCGGTATATTTATACCAG-
998095 TTACATTGT
189 TTACATTGT
*
998104 TAATGTACCTATTACATTATAATTATTGGTTTCGATGTTTTTTGGG-TCGATACTTTTAGAAAAT
1 AAATGTACCTATTACATTATAATTA-TGGTTTCGATG-TTTTTGGGATCGATACTTTTA-AAAAT
*
998168 GCATCGACAC
63 GTATCGACAC
998178 ATATTTATGT
Statistics
Matches: 232, Mismatches: 30, Indels: 22
0.82 0.11 0.08
Matches are distributed among these distances:
198 13 0.06
199 62 0.27
200 86 0.37
201 66 0.28
202 5 0.02
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.40
Consensus pattern (197 bp):
AAATGTACCTATTACATTATAATTATGGTTTCGATGTTTTTGGGATCGATACTTTTAAAAATGTA
TCGACACTTTATGAGTACACCCGTCTGGCATTCATTATGGACAAAATATATCGACACAAATTAAA
CAAGAATCGATACATTATGATGACCTATTTTCTAATAAAACCGGTATATTTATACCAGTTACATT
GT
Found at i:1001886 original size:200 final size:199
Alignment explanation
Indices: 1001478--1002237 Score: 817
Period size: 200 Copynumber: 3.8 Consensus size: 199
1001468 CGTTATTTAC
* * * * * * *
1001478 AAGTATCGACACAACACTAAAACGTGTCGATACATTATGTTCACCTATTTTCTCATAAAACCGAT
1 AAGTATCGACACAACATTAAAACGTGTCGACACATTATGTACACCTATTCTCACATAAAATCGGT
* ** * *
1001543 ACATTTATA-CGGTTACATTGTAAATTTACCTATT--ATTATAATTATCGGTTTCAATGTTTTTG
66 ACATTTATACCAGTTACATTACAAAATTACCTATTACATTATAATTATGGGTTTCAATGTTTTTG
* *
1001605 GGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTTCACCCTTCTTTGGGCATTCATTCT
131 GGATCGATACTTTTTAAAAATGTATCGACACTTTATGCGTT-AACCTT-TTTGGGCATTCATTCT
1001670 AGAAAA
194 AGAAAA
* * * * **
1001676 AAGCATCGACACATCAATTAAAA-GTGTCGACAAATTATGTAGACCTATTCTCACATAAAATTAG
1 AAGTATCGACACAAC-ATTAAAACGTGTCGACACATTATGTACACCTATTCTCACATAAAATCGG
* * * * *
1001740 TATATTTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATGGGTTT-GATGTTTTA
65 TACATTTATACCAGTTACATTACAAAATTACCTATTACATTATAATTATGGGTTTCAATGTTTTT
* * *** * *
1001804 GGGATCGATACTGTTTAAAAATGTATCGACACTTTATGGGTGTAACCTTTTTGGATTTTCCTTGT
130 GGGATCGATACTTTTTAAAAATGTATCGACACTTTATGCGT-TAACCTTTTTGGGCATTCATTCT
1001869 -GAACCAA
194 AGAA--AA
* * *
1001876 AAGTATCGACACAA-ATCTAAAACGTGTCGATACATTATGTTCACCTATTTTCTA-A-AAAGATC
1 AAGTATCGACACAACAT-TAAAACGTGTCGACACATTATGTACACCTATTCTC-ACATAAA-ATC
* * ** * * * * **
1001938 GGTACATTTGTACCAATTACATTGTAAATTTACATATTACATTATAATCATCGGTTTTGATGTTT
63 GGTACATTTATACCAGTTACATTACAAAATTACCTATTACATTATAATTATGGGTTTCAATGTTT
* * * *
1002003 TT-GG---GATACTTTTTATAAATGTATTGACACTTTATGCGTTCACCCTTTTGGGCATTCATTC
128 TTGGGATCGATACTTTTTAAAAATGTATCGACACTTTATGCGTTAACCTTTTTGGGCATTCATTC
1002064 TAGAAAA
193 TAGAAAA
* * * **
1002071 AAGTATCGACACAACATTAAAAAGTGTCGACACATTATGTAGACCGATTCTCACATAAAGCCGGT
1 AAGTATCGACACAACATTAAAACGTGTCGACACATTATGTACACCTATTCTCACATAAAATCGGT
* ** *
1002136 ATAAATATACCAGTTATATTACAAAATTACCTATTACATTATAATTATGGGTTTCAATGTTTTTG
66 ACATTTATACCAGTTACATTACAAAATTACCTATTACATTATAATTATGGGTTTCAATGTTTTTG
*
1002201 GGATCGATACTTTTTAAAAATGTATCGACCCTTTATG
131 GGATCGATACTTTTTAAAAATGTATCGACACTTTATG
1002238 GGAAACTTTA
Statistics
Matches: 455, Mismatches: 87, Indels: 39
0.78 0.15 0.07
Matches are distributed among these distances:
194 1 0.00
195 100 0.22
196 23 0.05
197 34 0.07
198 58 0.13
199 75 0.16
200 138 0.30
201 26 0.06
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (199 bp):
AAGTATCGACACAACATTAAAACGTGTCGACACATTATGTACACCTATTCTCACATAAAATCGGT
ACATTTATACCAGTTACATTACAAAATTACCTATTACATTATAATTATGGGTTTCAATGTTTTTG
GGATCGATACTTTTTAAAAATGTATCGACACTTTATGCGTTAACCTTTTTGGGCATTCATTCTAG
AAAA
Found at i:1002564 original size:25 final size:25
Alignment explanation
Indices: 1002535--1002587 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
1002525 GTACACAAGA
1002535 AATTTATACATAACAATGTTCAAAT
1 AATTTATACATAACAATGTTCAAAT
1002560 AATTTATACATAACAATGTTCAAAT
1 AATTTATACATAACAATGTTCAAAT
1002585 AAT
1 AAT
1002588 GTTCCCACAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.49, C:0.11, G:0.04, T:0.36
Consensus pattern (25 bp):
AATTTATACATAACAATGTTCAAAT
Found at i:1005657 original size:21 final size:21
Alignment explanation
Indices: 1005602--1005644 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
1005592 AGGGTGTCAA
*
1005602 AGTGCATCCATGCACTCCTGC
1 AGTGCATCCATGCACCCCTGC
1005623 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCCTGC
1005644 A
1 A
1005645 TTGCGTCCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.21, C:0.40, G:0.19, T:0.21
Consensus pattern (21 bp):
AGTGCATCCATGCACCCCTGC
Found at i:1005709 original size:23 final size:23
Alignment explanation
Indices: 1005678--1005739 Score: 106
Period size: 23 Copynumber: 2.7 Consensus size: 23
1005668 GCACCCCTGC
1005678 AGTGCATCGATGCACCTTCCACT
1 AGTGCATCGATGCACCTTCCACT
* *
1005701 AGTGTATCGATGCACCTTCTACT
1 AGTGCATCGATGCACCTTCCACT
1005724 AGTGCATCGATGCACC
1 AGTGCATCGATGCACC
1005740 ATGCAGTGCA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.23, C:0.31, G:0.19, T:0.27
Consensus pattern (23 bp):
AGTGCATCGATGCACCTTCCACT
Found at i:1008652 original size:21 final size:21
Alignment explanation
Indices: 1008626--1008703 Score: 147
Period size: 21 Copynumber: 3.7 Consensus size: 21
1008616 AGGGTGTCAA
*
1008626 AGTGCATCCATGCACTCCTGC
1 AGTGCATCCATGCACCCCTGC
1008647 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCCTGC
1008668 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCCTGC
1008689 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
1008704 TCCATTTCGA
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 56 1.00
ACGTcount: A:0.21, C:0.40, G:0.19, T:0.21
Consensus pattern (21 bp):
AGTGCATCCATGCACCCCTGC
Found at i:1009161 original size:34 final size:32
Alignment explanation
Indices: 1009122--1009191 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
1009112 TTTTGTAAAG
* *
1009122 GGGAAAGGTTCTAGCTTATCTCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCTCG-G-AAAAACTA
*
1009156 GGGAAAGGTTCTAGTTTAGCTCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCTCGGAAAAACTA
1009188 GGGA
1 GGGA
1009192 GTTGTAAGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 21 0.64
ACGTcount: A:0.31, C:0.13, G:0.30, T:0.26
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCTCGGAAAAACTA
Found at i:1009782 original size:200 final size:200
Alignment explanation
Indices: 1009433--1010001 Score: 967
Period size: 200 Copynumber: 2.8 Consensus size: 200
1009423 CCAACAATTA
* * *
1009433 TGGACAAAAAGTATCGACACAATATAAAAAATTGTCGATACATTATGTAAACCTATTCTCACATA
1 TGGACAAAAAGTATCGACACAAAATAAAAAAGTGTCGATACATTATGTAGACCTATTCTCACATA
* *
1009498 AAACCGGTATATTTATACCGGTTATATTACAAAATTACCTATTACGTTATAATTATCTGTTTCGA
66 AAACCGGTATATTTATACCAGTTATATTACAAAATTACCTATTACATTATAATTATCTGTTTCGA
* * *
1009563 TGTTTTTGGGATTGACACTTTTTATATATGTATCGACACTTTATTCGTTCATTATTTTTTGCATT
131 TGTTTTTGGGATCGACACTTTTTATATATGTATCGACACTTTATTCGTTCATCATTTTTGGCATT
1009628 CATTC
196 CATTC
* * *
1009633 TGGAAAAAAAGTATCGACGCAAAATAAAAAAGTGTCGATACATTTTGTAGACCTATTCTCACATA
1 TGGACAAAAAGTATCGACACAAAATAAAAAAGTGTCGATACATTATGTAGACCTATTCTCACATA
*
1009698 AAACCGATATATTTATACCAGTTATATTACAAAATTACCTATTACATTATAATTATCTGTTTCGA
66 AAACCGGTATATTTATACCAGTTATATTACAAAATTACCTATTACATTATAATTATCTGTTTCGA
* *
1009763 TGATTTTGGAATCGACACTTTTTATATATGTATCGACACTTTATTCGTTCATCATTTTTGGCATT
131 TGTTTTTGGGATCGACACTTTTTATATATGTATCGACACTTTATTCGTTCATCATTTTTGGCATT
1009828 CATTC
196 CATTC
*
1009833 TGGACAAAAAGTATCGACACAAAATAAAAAAGTGTCGATACATTATGTAGACATATTCTCACATA
1 TGGACAAAAAGTATCGACACAAAATAAAAAAGTGTCGATACATTATGTAGACCTATTCTCACATA
*
1009898 AAACCGGTATATTTATGCCAGTTATATTACAAAATTACCTATTACATTATAATTATCTGTTTCGA
66 AAACCGGTATATTTATACCAGTTATATTACAAAATTACCTATTACATTATAATTATCTGTTTCGA
* * *
1009963 TGTTTTTGGGATCGGCACGTTTTATAAATGTATCGACAC
131 TGTTTTTGGGATCGACACTTTTTATATATGTATCGACAC
1010002 ATATGCTCAC
Statistics
Matches: 344, Mismatches: 25, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
200 344 1.00
ACGTcount: A:0.34, C:0.16, G:0.12, T:0.38
Consensus pattern (200 bp):
TGGACAAAAAGTATCGACACAAAATAAAAAAGTGTCGATACATTATGTAGACCTATTCTCACATA
AAACCGGTATATTTATACCAGTTATATTACAAAATTACCTATTACATTATAATTATCTGTTTCGA
TGTTTTTGGGATCGACACTTTTTATATATGTATCGACACTTTATTCGTTCATCATTTTTGGCATT
CATTC
Found at i:1010293 original size:19 final size:19
Alignment explanation
Indices: 1010269--1010313 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
1010259 ATCCACATAA
1010269 AAAATTATAAATCGTATAC
1 AAAATTATAAATCGTATAC
*
1010288 AAAATTATAAATCTTATAC
1 AAAATTATAAATCGTATAC
1010307 AAAATTA
1 AAAATTA
1010314 ACTCTACATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.56, C:0.09, G:0.02, T:0.33
Consensus pattern (19 bp):
AAAATTATAAATCGTATAC
Found at i:1011890 original size:18 final size:18
Alignment explanation
Indices: 1011867--1011941 Score: 114
Period size: 18 Copynumber: 4.2 Consensus size: 18
1011857 TCCTCCTCAT
1011867 TTCCTCCATCTTTTCTTC
1 TTCCTCCATCTTTTCTTC
* *
1011885 TTCCTCCCTCTTTTCTTT
1 TTCCTCCATCTTTTCTTC
* *
1011903 TTCCTCCCTCTTTTCTTT
1 TTCCTCCATCTTTTCTTC
1011921 TTCCTCCATCTTTTCTTC
1 TTCCTCCATCTTTTCTTC
1011939 TTC
1 TTC
1011942 ATATTTTTTC
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 53 1.00
ACGTcount: A:0.03, C:0.39, G:0.00, T:0.59
Consensus pattern (18 bp):
TTCCTCCATCTTTTCTTC
Found at i:1012176 original size:33 final size:33
Alignment explanation
Indices: 1012125--1012196 Score: 117
Period size: 33 Copynumber: 2.2 Consensus size: 33
1012115 CCATCTTAAG
* *
1012125 TTCACCCCTCAACGCCTCAACTTCTTTCACCAC
1 TTCATCCCTCAACACCTCAACTTCTTTCACCAC
1012158 TTCATCCCTCAACACCTCAACTTCTTTCACCAC
1 TTCATCCCTCAACACCTCAACTTCTTTCACCAC
*
1012191 TCCATC
1 TTCATC
1012197 TATTTTTCCT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.22, C:0.47, G:0.01, T:0.29
Consensus pattern (33 bp):
TTCATCCCTCAACACCTCAACTTCTTTCACCAC
Found at i:1012249 original size:21 final size:21
Alignment explanation
Indices: 1012225--1012268 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
1012215 CCCATTATGC
1012225 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
1012246 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
1012267 CT
1 CT
1012269 TGATTGTCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.14, C:0.34, G:0.09, T:0.43
Consensus pattern (21 bp):
CTCTCAAGTTTCTCTTCGACT
Found at i:1014915 original size:182 final size:182
Alignment explanation
Indices: 1014606--1015824 Score: 1766
Period size: 182 Copynumber: 6.7 Consensus size: 182
1014596 TACGCGTACT
* * * * * ***
1014606 TATTAAAGTATTGACACTTTCAATATA-TCTGGTAGCGCTTTACCGGTTTTGTCATTTAGAGACC
1 TATTAAAGTATCGACACTTGCAATATATTC-GGTATCTCTTTACCGGTTTTGTCTTTTCCTGACC
* * * * *
1014670 AGTTTTATCATATTTTTACCTGTTATATCGTTATGGATCGATACATTTTTATAAAGTATCGACAC
65 GGTTTTGTCATATTTTTACCTGTTATATCGTTGTGGATCGATACATATTTATAAAGAATCGACAC
* * * *
1014735 TTTAAAGGCGCTAAAACAGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTA
130 TTTATAGGCGCTAAAACTGCTTCTCCTTTAAATTCACAATGTGTCGATACTTA
* * * ** *
1014788 TATTAAATTATCGACACTTTCAATATATTCGGTAGCTCTTTACCGGTTTTGTCTTTTCGAGATCG
1 TATTAAAGTATCGACACTTGCAATATATTCGGTATCTCTTTACCGGTTTTGTCTTTTCCTGACCG
* * * *
1014853 ATTTTATCATATTTTTACATGTTATATCGTTGTGGATCGATATATATTTATAAAGAATCGACACT
66 GTTTTGTCATATTTTTACCTGTTATATCGTTGTGGATCGATACATATTTATAAAGAATCGACACT
1014918 TTATAGGCGCTAAAACTGCTTCTCCTTTAAATTCACAATGTGTCGATACTTA
131 TTATAGGCGCTAAAACTGCTTCTCCTTTAAATTCACAATGTGTCGATACTTA
* *
1014970 TATTAAAGTATCGACACTTGCAATATATCCGGTATCTCTTTACCGGCTTTGTCTTTTCCTGACCG
1 TATTAAAGTATCGACACTTGCAATATATTCGGTATCTCTTTACCGGTTTTGTCTTTTCCTGACCG
* ** * *
1015035 GTTTTGTTATATTTTTGTCTGTTATATCGTTGTGGATTGATACATATTTATAAATAATCGACACT
66 GTTTTGTCATATTTTTACCTGTTATATCGTTGTGGATCGATACATATTTATAAAGAATCGACACT
** *
1015100 TTCCAGGCGCTAAAATTGCTTCTCCTTTAAATTCACAATGTGTCGATACTTA
131 TTATAGGCGCTAAAACTGCTTCTCCTTTAAATTCACAATGTGTCGATACTTA
* * *
1015152 TATTAAAGTATCGACACTTGCAATATA-TCTGGTATCTCTTTACTGATTTTATCTTTTCCTGACC
1 TATTAAAGTATCGACACTTGCAATATATTC-GGTATCTCTTTACCGGTTTTGTCTTTTCCTGACC
1015216 GGTTTTGTCATATTTTTACCTGTTATATCGTTGTGGATCGATACATATTTATAAAGAATCGACAC
65 GGTTTTGTCATATTTTTACCTGTTATATCGTTGTGGATCGATACATATTTATAAAGAATCGACAC
* * *
1015281 TTTCTAGGAGCTAAAACTGCTTCTCCTTTAAATTCACAATGTGTCGATATTTA
130 TTTATAGGCGCTAAAACTGCTTCTCCTTTAAATTCACAATGTGTCGATACTTA
* * *
1015334 TATTAAAGTATCGACACTTGCAATATA-TCATGTATCTCTTTATCGGTTTTATCTTTTCCTGACC
1 TATTAAAGTATCGACACTTGCAATATATTC-GGTATCTCTTTACCGGTTTTGTCTTTTCCTGACC
* *
1015398 GGTTTTGTCATATTTTTACCTGTTATATCGTTGTAGATCTATACATATTTATAAAGAATCGACAC
65 GGTTTTGTCATATTTTTACCTGTTATATCGTTGTGGATCGATACATATTTATAAAGAATCGACAC
1015463 TTTATAGGCGCTAAAACTGCTTCTCCTTTAAATTCACAATGTGTCGATACTTA
130 TTTATAGGCGCTAAAACTGCTTCTCCTTTAAATTCACAATGTGTCGATACTTA
* *
1015516 -ATTAAAGTATCGACACTTGCAATATATCCGGTATCTCTTTACCGGATTTGTCTTTTCCTGACCG
1 TATTAAAGTATCGACACTTGCAATATATTCGGTATCTCTTTACCGGTTTTGTCTTTTCCTGACCG
* *
1015580 GTTTTGTCATATTTTTACCTGTTATATCGTTGTGGATCGATACATATTTATAAAAAATTGACACT
66 GTTTTGTCATATTTTTACCTGTTATATCGTTGTGGATCGATACATATTTATAAAGAATCGACACT
* *
1015645 TTATAGGCGCTAAAACTGCTTCACCTTTAAATTCACTATGTGTCGATACTTA
131 TTATAGGCGCTAAAACTGCTTCTCCTTTAAATTCACAATGTGTCGATACTTA
* * * * * *
1015697 TATTAAAGTATCGACACGTGCAATATATACGGTAGCGCTTTACTGGTTTTGTCTTTTCGTGACCG
1 TATTAAAGTATCGACACTTGCAATATATTCGGTATCTCTTTACCGGTTTTGTCTTTTCCTGACCG
* * * * *
1015762 G-TTTGTTCATATTTTTTCCTTTTATATTGATGTGGATCGATACATTTTTATAAA-ATATCGACA
66 GTTTTG-TCATATTTTTACCTGTTATATCGTTGTGGATCGATACATATTTATAAAGA-ATCGACA
1015825 TAAACCGACA
Statistics
Matches: 946, Mismatches: 85, Indels: 12
0.91 0.08 0.01
Matches are distributed among these distances:
181 174 0.18
182 770 0.81
183 2 0.00
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.41
Consensus pattern (182 bp):
TATTAAAGTATCGACACTTGCAATATATTCGGTATCTCTTTACCGGTTTTGTCTTTTCCTGACCG
GTTTTGTCATATTTTTACCTGTTATATCGTTGTGGATCGATACATATTTATAAAGAATCGACACT
TTATAGGCGCTAAAACTGCTTCTCCTTTAAATTCACAATGTGTCGATACTTA
Found at i:1016085 original size:30 final size:31
Alignment explanation
Indices: 1016032--1016097 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 31
1016022 GGCTTTAGAT
*
1016032 AAATTTAAAGGTCAAATTGATATTTTATTTA
1 AAATTTAAAGGTCAAATTGATATTTTATCTA
**
1016063 AAATTTAGGGGTCAAA-TGATATTTTATCTA
1 AAATTTAAAGGTCAAATTGATATTTTATCTA
1016093 AAATT
1 AAATT
1016098 CATGAGGATA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
30 18 0.56
31 14 0.44
ACGTcount: A:0.41, C:0.05, G:0.12, T:0.42
Consensus pattern (31 bp):
AAATTTAAAGGTCAAATTGATATTTTATCTA
Found at i:1018658 original size:31 final size:31
Alignment explanation
Indices: 1018620--1018696 Score: 109
Period size: 31 Copynumber: 2.5 Consensus size: 31
1018610 TGTTATGTCG
*
1018620 GGGACCATATTGCAAACGGACTAAATGTTGA
1 GGGACCATATTGCAAACGAACTAAATGTTGA
* *
1018651 GGGACCATATTGAAAACGAACTAAATGTTGG
1 GGGACCATATTGCAAACGAACTAAATGTTGA
**
1018682 GGGATTATATTGCAA
1 GGGACCATATTGCAA
1018697 GTTTTAAAGT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.36, C:0.13, G:0.26, T:0.25
Consensus pattern (31 bp):
GGGACCATATTGCAAACGAACTAAATGTTGA
Found at i:1020742 original size:31 final size:30
Alignment explanation
Indices: 1020701--1020774 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 30
1020691 TAAAACTTGT
* * * *
1020701 AATATAATCCCCAAACATTTTGTCCGTTTGC
1 AATATGATCCCC-AACATTTAGTCCATTTAC
1020732 AATATGATCCCTCAACATTTAGTCCATTTAC
1 AATATGATCCC-CAACATTTAGTCCATTTAC
*
1020763 AATATGGTCCCC
1 AATATGATCCCC
1020775 GAAGTAACTG
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
30 1 0.03
31 35 0.95
32 1 0.03
ACGTcount: A:0.30, C:0.27, G:0.09, T:0.34
Consensus pattern (30 bp):
AATATGATCCCCAACATTTAGTCCATTTAC
Found at i:1021405 original size:32 final size:31
Alignment explanation
Indices: 1021359--1021459 Score: 96
Period size: 32 Copynumber: 3.2 Consensus size: 31
1021349 ACCCAAATAA
*
1021359 AAAATTAACTGATCTGATATTAACTCGATCCG
1 AAAATCAACTGATCTGATATTAACTCGA-CCG
* * * *
1021391 AAAATCAACCGATCTGACATTGACTCGACCC
1 AAAATCAACTGATCTGATATTAACTCGACCG
* *
1021422 AAAATCTAATTGATCCGATATTAA-TCTGACCCG
1 AAAATC-AACTGATCTGATATTAACTC-GA-CCG
1021455 AAAAT
1 AAAAT
1021460 TGACTAGACC
Statistics
Matches: 55, Mismatches: 11, Indels: 5
0.77 0.15 0.07
Matches are distributed among these distances:
31 10 0.18
32 38 0.69
33 7 0.13
ACGTcount: A:0.39, C:0.23, G:0.12, T:0.27
Consensus pattern (31 bp):
AAAATCAACTGATCTGATATTAACTCGACCG
Found at i:1021637 original size:3 final size:3
Alignment explanation
Indices: 1021565--1021621 Score: 114
Period size: 3 Copynumber: 19.0 Consensus size: 3
1021555 CAAAATTAAC
1021565 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1021613 AAT AAT AAT
1 AAT AAT AAT
1021622 CTATTCAAAT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1025294 original size:27 final size:27
Alignment explanation
Indices: 1025256--1025313 Score: 100
Period size: 27 Copynumber: 2.2 Consensus size: 27
1025246 GTCATTTCAG
*
1025256 ATGTCATTTATTGCAGCAATAATGCAT
1 ATGTCATTTATTGCAGAAATAATGCAT
1025283 ATGTCATTTATTGCAGAAATAATGCAT
1 ATGTCATTTATTGCAGAAATAATGCAT
1025310 -TGTC
1 ATGTC
1025314 CCAAATAGTG
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
26 4 0.13
27 26 0.87
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.38
Consensus pattern (27 bp):
ATGTCATTTATTGCAGAAATAATGCAT
Found at i:1027588 original size:27 final size:27
Alignment explanation
Indices: 1027550--1027607 Score: 109
Period size: 27 Copynumber: 2.2 Consensus size: 27
1027540 AGTAGCCAAA
1027550 CACACTACTTAATCACTCAACTAGAGT
1 CACACTACTTAATCACTCAACTAGAGT
1027577 CACACTACTTAATCACTCAACTAGAGT
1 CACACTACTTAATCACTCAACTAGAGT
1027604 -ACAC
1 CACAC
1027608 CATTTTTATT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 4 0.13
27 27 0.87
ACGTcount: A:0.38, C:0.31, G:0.07, T:0.24
Consensus pattern (27 bp):
CACACTACTTAATCACTCAACTAGAGT
Found at i:1027834 original size:13 final size:13
Alignment explanation
Indices: 1027791--1027836 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
1027781 ATTCTTAATT
*
1027791 TTATTTTTATTAA
1 TTATATTTATTAA
1027804 TTATAATTTA-T-A
1 TTAT-ATTTATTAA
1027816 -TATATTTATTAA
1 TTATATTTATTAA
1027828 TTATATTTA
1 TTATATTTA
1027837 ATGTTTATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
10 5 0.18
11 4 0.14
12 2 0.07
13 13 0.46
14 4 0.14
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
TTATATTTATTAA
Found at i:1033630 original size:20 final size:20
Alignment explanation
Indices: 1033605--1033697 Score: 87
Period size: 21 Copynumber: 4.5 Consensus size: 20
1033595 TTTTCCCAAT
*
1033605 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGAAAA
* * **
1033625 TCGCAACGCGTATTGGGAAAA
1 TCGCAATGCG-AATAAGAAAA
*
1033646 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGAAAA
* **
1033666 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGAAAA
1033687 TCGCAATGCGA
1 TCGCAATGCGA
1033698 TACTTACTAT
Statistics
Matches: 56, Mismatches: 15, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
20 26 0.46
21 30 0.54
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGAAAA
Found at i:1033650 original size:41 final size:41
Alignment explanation
Indices: 1033605--1033697 Score: 177
Period size: 41 Copynumber: 2.3 Consensus size: 41
1033595 TTTTCCCAAT
*
1033605 TCGCAATGCGAATAAGTAAATCGCAACGCGTATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1033646 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1033687 TCGCAATGCGA
1 TCGCAATGCGA
1033698 TACTTACTAT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:1033710 original size:41 final size:41
Alignment explanation
Indices: 1033624--1033759 Score: 139
Period size: 41 Copynumber: 3.3 Consensus size: 41
1033614 GAATAAGTAA
* ** *
1033624 ATCGCAACGCGTATTGGGAAAATCGCAATGCGAATAAGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTTACT
1033665 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
* * *** * *
1033706 ATCGCAATGCGATAATAAAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTTACT
*
1033748 TTCGCAACGCGA
1 ATCGCAACGCGA
1033760 TACTGACTTT
Statistics
Matches: 80, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
40 5 0.06
41 42 0.52
42 33 0.41
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.21
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
Found at i:1033711 original size:20 final size:20
Alignment explanation
Indices: 1033686--1033780 Score: 82
Period size: 20 Copynumber: 4.7 Consensus size: 20
1033676 AATTGGGAAA
*
1033686 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTTACT
* * * **
1033706 ATCGCAATGCGATAATAAAAAA
1 ATCGCAACGCGATACT--TACT
*
1033728 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTTACT
* *
1033748 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTTACT
*
1033768 TTCGCAACGCGAT
1 ATCGCAACGCGAT
1033781 TTACATAGCG
Statistics
Matches: 60, Mismatches: 13, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
20 46 0.77
22 14 0.23
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTTACT
Found at i:1034367 original size:19 final size:19
Alignment explanation
Indices: 1034345--1034529 Score: 165
Period size: 19 Copynumber: 10.1 Consensus size: 19
1034335 GAAACCAAAA
*
1034345 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1034364 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
1034383 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
1034402 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
1034422 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
1034438 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
1034455 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
1034469 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
* *
1034488 TCCGCGTTGTGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
1034508 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
1034528 TC
1 TC
1034530 AACCAGAAGA
Statistics
Matches: 136, Mismatches: 17, Indels: 26
0.76 0.09 0.15
Matches are distributed among these distances:
14 20 0.15
15 1 0.01
16 3 0.02
17 3 0.02
18 1 0.01
19 60 0.44
20 47 0.35
21 1 0.01
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1034422 original size:39 final size:38
Alignment explanation
Indices: 1034345--1034529 Score: 165
Period size: 33 Copynumber: 5.1 Consensus size: 38
1034335 GAAACCAAAA
*
1034345 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
*
1034383 TCGCGTTGCGATTTTTATTTCGCGGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGC-GTTGCGATTTTCATT
* * **
1034422 TCGCGTTGCGATTGTC---T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
* **
1034455 TCGCGTTGCGA--TTC---TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
* * *
1034488 TCCGCGTTGTGATTCTCATTATCTCGTTGCGATTTTCATT
1 T-CGCGTTGCGATTTTCATT-TCGCGTTGCGATTTTCATT
1034528 TC
1 TC
1034530 AACCAGAAGA
Statistics
Matches: 123, Mismatches: 14, Indels: 19
0.79 0.09 0.12
Matches are distributed among these distances:
31 3 0.02
33 38 0.31
34 9 0.07
35 1 0.01
36 3 0.02
38 21 0.17
39 30 0.24
40 18 0.15
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
Found at i:1034506 original size:20 final size:20
Alignment explanation
Indices: 1034472--1034529 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
1034462 GCGATTCTCT
**
1034472 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
* *
1034492 CGTTGTGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
*
1034512 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
1034530 AACCAGAAGA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
19 1 0.03
20 28 0.93
21 1 0.03
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.45
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCG
Found at i:1036590 original size:42 final size:42
Alignment explanation
Indices: 1036530--1036652 Score: 122
Period size: 42 Copynumber: 2.9 Consensus size: 42
1036520 GCCCGACTCG
* * *
1036530 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
1036572 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
1036614 ACTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
1036653 CCCGATTCAC
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
42 62 0.94
43 4 0.06
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.23
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:1036610 original size:21 final size:21
Alignment explanation
Indices: 1036586--1036652 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1036576 TCATTCCTCG
1036586 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
1036607 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
1036628 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
1036649 AGAG
1 AGAG
1036653 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:1038029 original size:14 final size:14
Alignment explanation
Indices: 1038010--1038045 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1038000 ATTGTTTAAT
1038010 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
1038024 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
1038038 TGATTTGT
1 TGATTTGT
1038046 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:1038246 original size:19 final size:19
Alignment explanation
Indices: 1038224--1038374 Score: 71
Period size: 19 Copynumber: 8.7 Consensus size: 19
1038214 CGAAATTAAA
1038224 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
**
1038243 TTCGTATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
1038258 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
1038276 TTCGCATTGCGA-----AA
1 TTCGCGTTGCGATTTTCAT
*
1038290 TTAGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
1038309 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
1038324 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
1038342 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
1038361 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
1038375 GGACATTAAG
Statistics
Matches: 93, Mismatches: 23, Indels: 31
0.63 0.16 0.21
Matches are distributed among these distances:
14 27 0.29
16 6 0.06
17 6 0.06
19 44 0.47
20 10 0.11
ACGTcount: A:0.15, C:0.22, G:0.21, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:1038270 original size:33 final size:32
Alignment explanation
Indices: 1038228--1038354 Score: 184
Period size: 33 Copynumber: 3.9 Consensus size: 32
1038218 ATTAAATTCG
*
1038228 CGTTGCGATTTTCATTTCGTATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
1038261 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
1038294 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
1038327 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
1038355 AGTAATTTCC
Statistics
Matches: 85, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
31 3 0.04
33 79 0.93
35 3 0.04
ACGTcount: A:0.15, C:0.22, G:0.20, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:1038318 original size:66 final size:66
Alignment explanation
Indices: 1038221--1038353 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 66
1038211 ACGCGAAATT
* *
1038221 AAATTCGCGTTGCGATTTTCATTTCGTATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1038286 G
66 G
*
1038287 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1038352 G
66 G
1038353 A
1 A
1038354 TAGTAATTTC
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.17, C:0.22, G:0.20, T:0.42
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:1040629 original size:12 final size:12
Alignment explanation
Indices: 1040612--1040636 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1040602 TCTTCGGGGA
1040612 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1040624 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1040636 C
1 C
1040637 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:1043198 original size:29 final size:29
Alignment explanation
Indices: 1043156--1043214 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
1043146 ATTTTCACCT
*
1043156 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATCGATGTAAGCAATGACATCAA
1043185 AACTAAATCGATGTAAGCAATGACATCAA
1 AACTAAATCGATGTAAGCAATGACATCAA
1043214 A
1 A
1043215 TTAATTTAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.49, C:0.15, G:0.14, T:0.22
Consensus pattern (29 bp):
AACTAAATCGATGTAAGCAATGACATCAA
Found at i:1047886 original size:29 final size:29
Alignment explanation
Indices: 1047844--1047902 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
1047834 ATTTTCACCT
1047844 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
1047873 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
1047902 A
1 A
1047903 TTAATTTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:1049062 original size:29 final size:29
Alignment explanation
Indices: 1049028--1049086 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
1049018 CCTAAATTAA
1049028 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
1049057 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
1049086 T
1 T
1049087 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:1053744 original size:29 final size:29
Alignment explanation
Indices: 1053710--1053768 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
1053700 CCTAAATTAA
1053710 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
1053739 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
1053768 T
1 T
1053769 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:1063678 original size:31 final size:31
Alignment explanation
Indices: 1063608--1063678 Score: 106
Period size: 31 Copynumber: 2.3 Consensus size: 31
1063598 CTTTTAAAAC
* *
1063608 TTGCAATACAGTCTCCCAACATTTAGTCCGT
1 TTGCAATATAGTCCCCCAACATTTAGTCCGT
* *
1063639 TTGCAATATAGTCCCCCAATATTTAGTCTGT
1 TTGCAATATAGTCCCCCAACATTTAGTCCGT
1063670 TTGCAATAT
1 TTGCAATAT
1063679 GGTCTCTGAC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.27, C:0.24, G:0.13, T:0.37
Consensus pattern (31 bp):
TTGCAATATAGTCCCCCAACATTTAGTCCGT
Found at i:1065398 original size:23 final size:23
Alignment explanation
Indices: 1065372--1065446 Score: 141
Period size: 23 Copynumber: 3.3 Consensus size: 23
1065362 ATGGACCCTT
1065372 ATTCAAGTCAACACCTCCACATA
1 ATTCAAGTCAACACCTCCACATA
1065395 ATTCAAGTCAACACCTCCACATA
1 ATTCAAGTCAACACCTCCACATA
*
1065418 ATTCAAGTCAATACCTCCACATA
1 ATTCAAGTCAACACCTCCACATA
1065441 ATTCAA
1 ATTCAA
1065447 AGTTAGATTA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.40, C:0.32, G:0.04, T:0.24
Consensus pattern (23 bp):
ATTCAAGTCAACACCTCCACATA
Found at i:1065705 original size:30 final size:30
Alignment explanation
Indices: 1065671--1065750 Score: 97
Period size: 30 Copynumber: 2.6 Consensus size: 30
1065661 GCGTCAAACG
*
1065671 GTTGGGGACCATATTGTAAACAGATTAAAT
1 GTTGGGGACCATATTGTAAACAGACTAAAT
* * *
1065701 GTTGGGGATCATATTGCAAACGGACTAAAT
1 GTTGGGGACCATATTGTAAACAGACTAAAT
**
1065731 GTTGGGAGACTGTATTGTAA
1 GTTGGG-GACCATATTGTAA
1065751 GTTTTAAAAG
Statistics
Matches: 41, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
30 32 0.78
31 9 0.22
ACGTcount: A:0.33, C:0.10, G:0.28, T:0.30
Consensus pattern (30 bp):
GTTGGGGACCATATTGTAAACAGACTAAAT
Found at i:1072687 original size:2 final size:2
Alignment explanation
Indices: 1072680--1072704 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1072670 ATATGTGTAC
1072680 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1072705 CGAATATACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1074431 original size:132 final size:133
Alignment explanation
Indices: 1074063--1074436 Score: 426
Period size: 130 Copynumber: 2.8 Consensus size: 133
1074053 GCTCATCCGC
* * *
1074063 GATGAAGAGAATCTTGGCCATCTTAGGAAAGATGATAACATGGTTCC-ACTGC--TGGGGACGGC
1 GATGAAGAG-TTCTTGGCCATCTTAGG-AAGGTGATAACATGGTTCCTAC-GCGATGAGGACGGC
* * * * * **
1074125 TGGTTATCTGAGGTTGACACGGCTCATACGTGATGAAGAGTTCTGGTCAGGGGATGACATTACTC
63 TGGTTATCTAAGGTTGACACGGCTCCTACGTGATGAGGAGATCTGGTCAGAGGATGACACGACTC
1074190 ATACAT
128 ATACAT
* *
1074196 GATGAAGAGTTCTTGGCCATC-TA--AAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGG
1 GATGAAGAGTTCTTGGCCATCTTAGGAAGGTGATAACATGGTTCCTACGCGATGAGGACGGCTGG
* * *
1074258 TTATCTAAGGGTGACACGGTTCCTACGTGATGAGGAAATCTGGTC-GAAGGATGACACGACTCAT
66 TTATCTAAGGTTGACACGGCTCCTACGTGATGAGGAGATCTGGTCAG-AGGATGACACGACTCAT
* *
1074322 GCGT
130 ACAT
*
1074326 GA-G-AGAGTTCTTGGCCATCTTTAGGAAGGGTGATAACTTGGTTCCTACGCGATGAGGACGG-T
1 GATGAAGAGTTCTTGGCCATC-TTAGGAA-GGTGATAACATGGTTCCTACGCGATGAGGACGGCT
* ***
1074388 GGTTATCTAATGTTGACGTTGCTCCTACGTGATGAGGAGATCTGGTCAG
64 GGTTATCTAAGGTTGACACGGCTCCTACGTGATGAGGAGATCTGGTCAG
1074437 CTGATGTTGA
Statistics
Matches: 204, Mismatches: 27, Indels: 20
0.81 0.11 0.08
Matches are distributed among these distances:
128 34 0.17
129 4 0.02
130 70 0.34
131 2 0.01
132 54 0.26
133 40 0.20
ACGTcount: A:0.25, C:0.17, G:0.31, T:0.27
Consensus pattern (133 bp):
GATGAAGAGTTCTTGGCCATCTTAGGAAGGTGATAACATGGTTCCTACGCGATGAGGACGGCTGG
TTATCTAAGGTTGACACGGCTCCTACGTGATGAGGAGATCTGGTCAGAGGATGACACGACTCATA
CAT
Found at i:1075352 original size:8 final size:8
Alignment explanation
Indices: 1075330--1075375 Score: 60
Period size: 7 Copynumber: 5.9 Consensus size: 8
1075320 TCCTTTATTT
1075330 ATTTTTTC
1 ATTTTTTC
*
1075338 TTCTTTTTC
1 AT-TTTTTC
1075347 A-TTTTTC
1 ATTTTTTC
1075354 A-TTTTTC
1 ATTTTTTC
1075361 ATTTTTTC
1 ATTTTTTC
1075369 ATTTTTT
1 ATTTTTT
1075376 TTTTTTTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
7 14 0.41
8 14 0.41
9 6 0.18
ACGTcount: A:0.11, C:0.13, G:0.00, T:0.76
Consensus pattern (8 bp):
ATTTTTTC
Found at i:1075359 original size:15 final size:14
Alignment explanation
Indices: 1075341--1075374 Score: 59
Period size: 15 Copynumber: 2.4 Consensus size: 14
1075331 TTTTTTCTTC
1075341 TTTTTCATTTTTCA
1 TTTTTCATTTTTCA
1075355 TTTTTCATTTTTTCA
1 TTTTTCA-TTTTTCA
1075370 TTTTT
1 TTTTT
1075375 TTTTTTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 7 0.37
15 12 0.63
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTTTCATTTTTCA
Found at i:1075374 original size:1 final size:1
Alignment explanation
Indices: 1075370--1075395 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
1075360 CATTTTTTCA
1075370 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
1075396 AAGTGTAATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:1075380 original size:15 final size:15
Alignment explanation
Indices: 1075348--1075395 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
1075338 TTCTTTTTCA
**
1075348 TTTTTCATTTTTCAT
1 TTTTTCATTTTTTTT
1075363 TTTTTCATTTTTTTT
1 TTTTTCATTTTTTTT
1075378 TTTTT--TTTTTTTT
1 TTTTTCATTTTTTTT
1075391 TTTTT
1 TTTTT
1075396 AAGTGTAATC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
13 13 0.42
15 18 0.58
ACGTcount: A:0.06, C:0.06, G:0.00, T:0.88
Consensus pattern (15 bp):
TTTTTCATTTTTTTT
Found at i:1076234 original size:178 final size:175
Alignment explanation
Indices: 1075912--1076261 Score: 657
Period size: 178 Copynumber: 2.0 Consensus size: 175
1075902 TTCCTTCATT
1075912 AATCGTTGTTCAAATTCAATGCATTTCTGTGATGATCCTTTCAGGTGTTCCATATCTACAAATGA
1 AATCGTTGTTCAAATTCAATGCATTTCTGTGATGATCCTTTCAGGTGTTCCATATCTACAAATGA
1075977 TTTCTCTTTTAGAAATCTGCATACTGCTCCTTTGTGACATTAGCATAAGAGGCAGCTTCAACCCA
66 TTTCTCTTTTAGAAATCTGCATACTGCTCCTTTGTGACATTAGCATAAGAGGCAGCTTCAACCCA
1076042 TTTGGTGAAGTAGTCTATAGCCACTAAGATAAAACGATGTCCCTA
131 TTTGGTGAAGTAGTCTATAGCCACTAAGATAAAACGATGTCCCTA
1076087 AATCGTTGTTC-AATTCAATGCATTATCTGTGATGATCCTTTCAGGTGTTCCATATCTACAAAAT
1 AATCGTTGTTCAAATTCAATGCATT-TCTGTGATGATCCTTTCAGGTGTTCCATATCTAC-AAAT
1076151 GATTTCTCTTTTTAGAAATCTGCATACTGCTCCTTTTGTGACATTAGCATAAGAGGCAGCTTCAA
64 GATTTCTC-TTTTAGAAATCTGCATACTGCTCC-TTTGTGACATTAGCATAAGAGGCAGCTTCAA
1076216 CCCATTTGGTGAAGTAGTCTATAGCCACTAAGATAAAACGATGTCC
127 CCCATTTGGTGAAGTAGTCTATAGCCACTAAGATAAAACGATGTCC
1076262 ATTTGAGGCC
Statistics
Matches: 171, Mismatches: 0, Indels: 5
0.97 0.00 0.03
Matches are distributed among these distances:
174 13 0.08
175 45 0.26
176 12 0.07
177 24 0.14
178 77 0.45
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.35
Consensus pattern (175 bp):
AATCGTTGTTCAAATTCAATGCATTTCTGTGATGATCCTTTCAGGTGTTCCATATCTACAAATGA
TTTCTCTTTTAGAAATCTGCATACTGCTCCTTTGTGACATTAGCATAAGAGGCAGCTTCAACCCA
TTTGGTGAAGTAGTCTATAGCCACTAAGATAAAACGATGTCCCTA
Found at i:1077100 original size:21 final size:21
Alignment explanation
Indices: 1077074--1077116 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
1077064 ACTAGTAAAA
1077074 GGATAATGATCTCCCTCAGGT
1 GGATAATGATCTCCCTCAGGT
1077095 GGATAATGATCTCCCTCAGGT
1 GGATAATGATCTCCCTCAGGT
1077116 G
1 G
1077117 AAACTAGTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.23, C:0.23, G:0.26, T:0.28
Consensus pattern (21 bp):
GGATAATGATCTCCCTCAGGT
Found at i:1085196 original size:13 final size:13
Alignment explanation
Indices: 1085178--1085202 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1085168 TACACACTCA
1085178 AAAATAAATAAAT
1 AAAATAAATAAAT
1085191 AAAATAAATAAA
1 AAAATAAATAAA
1085203 AGGTTAGAGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (13 bp):
AAAATAAATAAAT
Found at i:1096047 original size:23 final size:25
Alignment explanation
Indices: 1095998--1096081 Score: 68
Period size: 26 Copynumber: 3.4 Consensus size: 25
1095988 CAATAAAAAC
*
1095998 AATTAAATAATAAAAGCAATTCGAAT
1 AATTAAATAATAAAAACAATTC-AAT
*
1096024 AATTAAATATTAAAAAC-ATT-AAT
1 AATTAAATAATAAAAACAATTCAAT
** *
1096047 AAACAAAATAAATAAAAA-AA-TCCAT
1 -AATTAAAT-AATAAAAACAATTCAAT
1096072 AATTAAATAA
1 AATTAAATAA
1096082 AAACGTTACA
Statistics
Matches: 46, Mismatches: 8, Indels: 11
0.71 0.12 0.17
Matches are distributed among these distances:
23 5 0.11
24 13 0.28
25 13 0.28
26 15 0.33
ACGTcount: A:0.64, C:0.07, G:0.02, T:0.26
Consensus pattern (25 bp):
AATTAAATAATAAAAACAATTCAAT
Found at i:1102674 original size:23 final size:22
Alignment explanation
Indices: 1102645--1102712 Score: 63
Period size: 23 Copynumber: 3.2 Consensus size: 22
1102635 TTTTGTGACT
1102645 ACAACATGATCTAGTGTTAGTCA
1 ACAACATGATCTAGTGTT-GTCA
* * *
1102668 ACGACAT-ATCT--TG-TGACT
1 ACAACATGATCTAGTGTTGTCA
1102686 ACAACATGATCTAGTGTTGGTCA
1 ACAACATGATCTAGTGTT-GTCA
1102709 ACAA
1 ACAA
1102713 GGTATCTTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 10
0.68 0.12 0.20
Matches are distributed among these distances:
18 8 0.24
19 5 0.15
20 2 0.06
21 2 0.06
22 5 0.15
23 12 0.35
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29
Consensus pattern (22 bp):
ACAACATGATCTAGTGTTGTCA
Found at i:1102694 original size:41 final size:41
Alignment explanation
Indices: 1102637--1102737 Score: 157
Period size: 41 Copynumber: 2.5 Consensus size: 41
1102627 AACCATTTTT
*
1102637 TTGTGACTACAACATGATCTAGTGTTAGTCAACGACATATC
1 TTGTGACTACAACATGATCTAGTGTTAGTCAACAACATATC
* **
1102678 TTGTGACTACAACATGATCTAGTGTTGGTCAACAAGGTATC
1 TTGTGACTACAACATGATCTAGTGTTAGTCAACAACATATC
*
1102719 TTTTGACTACAACATGATC
1 TTGTGACTACAACATGATC
1102738 ATACTTCCTG
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 55 1.00
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.33
Consensus pattern (41 bp):
TTGTGACTACAACATGATCTAGTGTTAGTCAACAACATATC
Found at i:1104200 original size:24 final size:24
Alignment explanation
Indices: 1104121--1104206 Score: 102
Period size: 24 Copynumber: 3.6 Consensus size: 24
1104111 TTTACGGTTG
*
1104121 TTTGTGTTCGTTTACGTTCGTTTA
1 TTTGTGTTCGTTTATGTTCGTTTA
* *
1104145 -TTGTGTTTGTTTATGTTCATTTA
1 TTTGTGTTCGTTTATGTTCGTTTA
* ** *
1104168 TATCCGTTCGTTTATGTTCGTTAA
1 TTTGTGTTCGTTTATGTTCGTTTA
1104192 TTTGTGTTCGTTTAT
1 TTTGTGTTCGTTTAT
1104207 CATTTAAATG
Statistics
Matches: 49, Mismatches: 12, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
23 20 0.41
24 29 0.59
ACGTcount: A:0.12, C:0.10, G:0.19, T:0.59
Consensus pattern (24 bp):
TTTGTGTTCGTTTATGTTCGTTTA
Found at i:1105753 original size:14 final size:14
Alignment explanation
Indices: 1105736--1105762 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1105726 AATCAAAATA
1105736 ATTATTAAAAATTT
1 ATTATTAAAAATTT
1105750 ATTATTAAAAATT
1 ATTATTAAAAATT
1105763 AGATAATTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
ATTATTAAAAATTT
Found at i:1105906 original size:2 final size:2
Alignment explanation
Indices: 1105836--1105891 Score: 105
Period size: 2 Copynumber: 28.5 Consensus size: 2
1105826 ATCCTAAATC
1105836 TA TA -A 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
1105877 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
1105892 TGGTTTTGAA
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 52 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1108326 original size:106 final size:106
Alignment explanation
Indices: 1108141--1108357 Score: 353
Period size: 106 Copynumber: 2.0 Consensus size: 106
1108131 TGTATTGTTC
* * *
1108141 CGAGTCCAATATCCTCCGCCGTGAAATTGAAATTGGTTCTGGAACCGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTCCGCCGTGAAATTGAAATTGGCTCTGAAACCGGGAAATGGTTTGTTGACA
1108206 ACCAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
66 ACCAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * * **
1108247 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATGGTTTGTTGACA
1 CGAGTCCAATATCCTCCGCCGTGAAATTGAAATTGGCTCTGAAACCGGGAAATGGTTTGTTGACA
1108312 ACCAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
66 ACCAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
*
1108353 TGAGT
1 CGAGT
1108358 GGCACGATAT
Statistics
Matches: 102, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
106 102 1.00
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.34
Consensus pattern (106 bp):
CGAGTCCAATATCCTCCGCCGTGAAATTGAAATTGGCTCTGAAACCGGGAAATGGTTTGTTGACA
ACCAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
Found at i:1108885 original size:18 final size:18
Alignment explanation
Indices: 1108858--1108893 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1108848 TGTTGAATCC
*
1108858 CCAAAGATGCCCCAATAT
1 CCAAAAATGCCCCAATAT
1108876 CCAAAAATGCCCCAATAT
1 CCAAAAATGCCCCAATAT
1108894 TTGATGTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.42, C:0.33, G:0.08, T:0.17
Consensus pattern (18 bp):
CCAAAAATGCCCCAATAT
Found at i:1109337 original size:22 final size:22
Alignment explanation
Indices: 1109311--1109364 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
1109301 GTGTTTGGTT
1109311 AAAGGTTTGACATTTGATGCTC
1 AAAGGTTTGACATTTGATGCTC
*
1109333 AAAGGTTTGGCATTTGATGCTC
1 AAAGGTTTGACATTTGATGCTC
*
1109355 GAAGGTTTGA
1 AAAGGTTTGA
1109365 TGGGGTAGCC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.26, C:0.11, G:0.28, T:0.35
Consensus pattern (22 bp):
AAAGGTTTGACATTTGATGCTC
Found at i:1110025 original size:8 final size:7
Alignment explanation
Indices: 1110013--1110082 Score: 61
Period size: 8 Copynumber: 9.1 Consensus size: 7
1110003 TGATTTTTGC
1110013 TTCTTTT
1 TTCTTTT
*
1110020 CTTCTTTG
1 -TTCTTTT
1110028 TTCTTGTT
1 TTCTT-TT
1110036 TT-TTTT
1 TTCTTTT
1110042 TTCCTTTT
1 TT-CTTTT
1110050 TTCCTTTT
1 TT-CTTTT
1110058 TTGCTTCTT
1 TT-CTT-TT
1110067 TTCTTTTT
1 TTC-TTTT
1110075 TTCTTTT
1 TTCTTTT
1110082 T
1 T
1110083 GCCCTTTTTA
Statistics
Matches: 54, Mismatches: 3, Indels: 11
0.79 0.04 0.16
Matches are distributed among these distances:
6 4 0.07
7 12 0.22
8 32 0.59
9 6 0.11
ACGTcount: A:0.00, C:0.17, G:0.04, T:0.79
Consensus pattern (7 bp):
TTCTTTT
Found at i:1110051 original size:41 final size:40
Alignment explanation
Indices: 1110006--1110091 Score: 97
Period size: 40 Copynumber: 2.1 Consensus size: 40
1109996 GTCCTTTTGA
* *
1110006 TTTTTGCTTCTTTT-CTTCTTTGTTCTTGTTTTT-TTTTT-CCT
1 TTTTTCCTT-TTTTGCTTC-TT-TTCTT-TTTTTCTTTTTGCCC
1110047 TTTTTCCTTTTTTGCTTCTTTTCTTTTTTTCTTTTTGCCC
1 TTTTTCCTTTTTTGCTTCTTTTCTTTTTTTCTTTTTGCCC
1110087 TTTTT
1 TTTTT
1110092 ATTCTGATTG
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
38 5 0.12
39 10 0.25
40 13 0.32
41 12 0.30
ACGTcount: A:0.00, C:0.19, G:0.06, T:0.76
Consensus pattern (40 bp):
TTTTTCCTTTTTTGCTTCTTTTCTTTTTTTCTTTTTGCCC
Found at i:1110074 original size:33 final size:32
Alignment explanation
Indices: 1110006--1110096 Score: 87
Period size: 32 Copynumber: 2.8 Consensus size: 32
1109996 GTCCTTTTGA
* * *
1110006 TTTTTGCTTCTTTT-CTTCTTTGTTCTTGTTTT
1 TTTTTTCTT-TTTTCCTTTTTTGTTCTTGTTCT
1110038 TTTTTTCCTTTTTTCCTTTTTTGCTTCTT-TTCT
1 TTTTTT-CTTTTTTCCTTTTTTG-TTCTTGTTCT
* * *
1110071 TTTTTTCTTTTTGCCCTTTTTATTCT
1 TTTTTTCTTTTTTCCTTTTTTGTTCT
1110097 GATTGAATCT
Statistics
Matches: 50, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
31 4 0.08
32 22 0.44
33 19 0.38
34 5 0.10
ACGTcount: A:0.01, C:0.19, G:0.05, T:0.75
Consensus pattern (32 bp):
TTTTTTCTTTTTTCCTTTTTTGTTCTTGTTCT
Found at i:1113531 original size:46 final size:46
Alignment explanation
Indices: 1113478--1113570 Score: 177
Period size: 46 Copynumber: 2.0 Consensus size: 46
1113468 GAATTCTGTA
*
1113478 TATTAAGGAATAAAGTTATTCCTTAAATCTAGGAGTTAACTTAGAC
1 TATTAAGGAATAAAATTATTCCTTAAATCTAGGAGTTAACTTAGAC
1113524 TATTAAGGAATAAAATTATTCCTTAAATCTAGGAGTTAACTTAGAC
1 TATTAAGGAATAAAATTATTCCTTAAATCTAGGAGTTAACTTAGAC
1113570 T
1 T
1113571 TGATATTCTC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.35
Consensus pattern (46 bp):
TATTAAGGAATAAAATTATTCCTTAAATCTAGGAGTTAACTTAGAC
Found at i:1125328 original size:44 final size:44
Alignment explanation
Indices: 1125273--1125356 Score: 120
Period size: 44 Copynumber: 1.9 Consensus size: 44
1125263 TAATAATGTA
1125273 ATTAGTAATTTAAT-ATATTT-AATTATCTATTAGA-AAATTAATAG
1 ATTAGTAATTT-ATCAT-TTTCAATTATCTATTA-ACAAATTAATAG
1125317 ATTAGTAATTTATCATTTTCAATTATCTATTAACAAATTA
1 ATTAGTAATTTATCATTTTCAATTATCTATTAACAAATTA
1125357 GTAATTTTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
43 6 0.16
44 31 0.84
ACGTcount: A:0.43, C:0.06, G:0.05, T:0.46
Consensus pattern (44 bp):
ATTAGTAATTTATCATTTTCAATTATCTATTAACAAATTAATAG
Found at i:1137702 original size:20 final size:20
Alignment explanation
Indices: 1137677--1137714 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1137667 CTTTATTTGA
*
1137677 ATTAATCAAATAATAATACT
1 ATTAATCAAATAAGAATACT
1137697 ATTAATCAAATAAGAATA
1 ATTAATCAAATAAGAATA
1137715 AAATATATAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.58, C:0.08, G:0.03, T:0.32
Consensus pattern (20 bp):
ATTAATCAAATAAGAATACT
Found at i:1142550 original size:20 final size:20
Alignment explanation
Indices: 1142521--1142560 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1142511 AGTATGCTCG
1142521 GAGGGAACCGATTCCCCCCA
1 GAGGGAACCGATTCCCCCCA
*
1142541 GAGGGTACCGATTCCCCCCA
1 GAGGGAACCGATTCCCCCCA
1142561 CTGTTCAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.23, C:0.40, G:0.25, T:0.12
Consensus pattern (20 bp):
GAGGGAACCGATTCCCCCCA
Found at i:1148253 original size:20 final size:20
Alignment explanation
Indices: 1148228--1148265 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1148218 TTTTGGTGCA
*
1148228 GAGGGAATCGATACCCCCAT
1 GAGGGAACCGATACCCCCAT
*
1148248 GAGGGAACCGATTCCCCC
1 GAGGGAACCGATACCCCC
1148266 TTGGGGTTCT
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:0.26, C:0.34, G:0.26, T:0.13
Consensus pattern (20 bp):
GAGGGAACCGATACCCCCAT
Found at i:1154038 original size:46 final size:46
Alignment explanation
Indices: 1153985--1154083 Score: 162
Period size: 46 Copynumber: 2.1 Consensus size: 46
1153975 GTAAACAATT
*
1153985 TAATATTGTTTAAGTAAAGATTCATGTTCGAGCCCTTATATATATA
1 TAATATTGTTTAAGTAAAGATTCATGTTCGAGCCCTCATATATATA
**
1154031 TAATATTGTTTAAGTAAAGATTCATGTTCGAGTTCTCATATATATA
1 TAATATTGTTTAAGTAAAGATTCATGTTCGAGCCCTCATATATATA
1154077 TATATAT
1 TA-ATAT
1154084 ATATATATAT
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
46 45 0.92
47 4 0.08
ACGTcount: A:0.35, C:0.09, G:0.12, T:0.43
Consensus pattern (46 bp):
TAATATTGTTTAAGTAAAGATTCATGTTCGAGCCCTCATATATATA
Found at i:1154075 original size:2 final size:2
Alignment explanation
Indices: 1154068--1154150 Score: 166
Period size: 2 Copynumber: 41.5 Consensus size: 2
1154058 TCGAGTTCTC
1154068 AT 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 AT
1154110 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1154151 ATCTCTGTTG
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 81 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1154474 original size:2 final size:2
Alignment explanation
Indices: 1154467--1154526 Score: 104
Period size: 2 Copynumber: 30.5 Consensus size: 2
1154457 TTTATTTAGA
1154467 AT 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 AT
*
1154509 AT AT AT GT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT A
1154527 ATTTTGAAAA
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
1 1 0.02
2 54 0.98
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1154615 original size:36 final size:36
Alignment explanation
Indices: 1154511--1154874 Score: 390
Period size: 38 Copynumber: 9.7 Consensus size: 36
1154501 ATATATATAT
* * *
1154511 ATATGTATATTATATAATTTTGAAAACATTTTGAAA
1 ATATATATATTATATAGTTTTTAAAACATTTTGAAA
*
1154547 ATATATA-A-TATATAATTTTTAAAAACATTTTGAAA
1 ATATATATATTATATAGTTTTT-AAAACATTTTGAAA
*
1154582 ACATATATATTATATAGTTTTTAAAACATTTTGAAAA
1 ATATATATATTATATAGTTTTTAAAACATTTTG-AAA
1154619 TATATATATATTATATAGTTTTTAAAACATTTTGAAA
1 -ATATATATATTATATAGTTTTTAAAACATTTTGAAA
1154656 ATATATATATTATATAGTTTTTAAAACATTTTGAAAA
1 ATATATATATTATATAGTTTTTAAAACATTTTG-AAA
* * *
1154693 CATATGTATATTATATAATTTTTAAAACATTTTAATATA
1 -ATATATATATTATATAGTTTTTAAAACATTTTGA-A-A
* * *
1154732 TATATATATATTATATAATTTTTAAAACGTTTTTAAAAAA
1 -ATATATATATTATATAGTTTTTAAAAC-ATTTT--GAAA
* *
1154772 ATATATATATAATATATGGTTTTAAAACAATTTTTGAAA
1 ATATATATATTATATA-GTTTTTAAAAC-A-TTTTGAAA
* * * **
1154811 ATATATATAATATATAGTTTTGAAAATTATTTTTTTAA
1 ATATATATATTATATAGTTTTTAAAA-CA-TTTTGAAA
* *
1154849 AGATATATATTATATAGTTTTAAAAA
1 ATATATATATTATATAGTTTTTAAAA
1154875 TGTTCTTCAT
Statistics
Matches: 286, Mismatches: 27, Indels: 28
0.84 0.08 0.08
Matches are distributed among these distances:
34 11 0.04
35 21 0.07
36 51 0.18
37 21 0.07
38 102 0.36
39 59 0.21
40 14 0.05
41 5 0.02
42 2 0.01
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (36 bp):
ATATATATATTATATAGTTTTTAAAACATTTTGAAA
Found at i:1154730 original size:27 final size:28
Alignment explanation
Indices: 1154683--1154737 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 28
1154673 TTTTTAAAAC
1154683 ATTTTGAAAACATATGTATAT-TATATA
1 ATTTTGAAAACATATGTATATATATATA
* *
1154710 ATTTTTAAAACAT-TTTAATATATATATA
1 ATTTTGAAAACATATGT-ATATATATATA
1154738 TATATTATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 2 0.08
27 16 0.67
28 6 0.25
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (28 bp):
ATTTTGAAAACATATGTATATATATATA
Found at i:1154916 original size:19 final size:19
Alignment explanation
Indices: 1154889--1154929 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1154879 CTTCATTGTA
1154889 TTTACTTATTA-TTATTTAT
1 TTTACTTATTACTTA-TTAT
*
1154908 TTTATTTATTACTTATTAT
1 TTTACTTATTACTTATTAT
1154927 TTT
1 TTT
1154930 TTCTTTTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 17 0.85
20 3 0.15
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (19 bp):
TTTACTTATTACTTATTAT
Found at i:1156005 original size:8 final size:8
Alignment explanation
Indices: 1155992--1156017 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
1155982 TTCAAAACGT
1155992 TTTTTTTA
1 TTTTTTTA
1156000 TTTTTTTA
1 TTTTTTTA
1156008 TTTTTTTA
1 TTTTTTTA
1156016 TT
1 TT
1156018 CTCCAATGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (8 bp):
TTTTTTTA
Found at i:1156123 original size:18 final size:18
Alignment explanation
Indices: 1156102--1156154 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
1156092 TTTATCTCCA
1156102 TTTATTTATTTATTTTTC
1 TTTATTTATTTATTTTTC
*
1156120 TTTA-TTATTTTTCTTTTC
1 TTTATTTATTTAT-TTTTC
1156138 TCTTAATTTA-TTATTTT
1 T-TT-ATTTATTTATTTT
1156155 AGTATTATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
17 7 0.24
18 10 0.34
19 5 0.17
20 4 0.14
21 3 0.10
ACGTcount: A:0.17, C:0.08, G:0.00, T:0.75
Consensus pattern (18 bp):
TTTATTTATTTATTTTTC
Found at i:1156129 original size:13 final size:14
Alignment explanation
Indices: 1156106--1156135 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
1156096 TCTCCATTTA
1156106 TTTATTTATTTTTC
1 TTTATTTATTTTTC
1156120 TTTA-TTATTTTTC
1 TTTATTTATTTTTC
1156133 TTT
1 TTT
1156136 TCTCTTAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.13, C:0.07, G:0.00, T:0.80
Consensus pattern (14 bp):
TTTATTTATTTTTC
Found at i:1156177 original size:3 final size:3
Alignment explanation
Indices: 1156145--1156200 Score: 66
Period size: 3 Copynumber: 19.7 Consensus size: 3
1156135 TTCTCTTAAT
*
1156145 TTA TTA TT- TTA GTA TTA -TA TT- TGT- TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA
1156187 TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TT
1156201 TCCTTCTTTT
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
2 6 0.13
3 41 0.87
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.68
Consensus pattern (3 bp):
TTA
Done.