Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015299.1 Kokia drynarioides strain JFW-HI SEQ_130344, 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: 1333876
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 300 characters in sequence are not A, C, G, or T
File 4 of 4
Found at i:1179651 original size:6 final size:6
Alignment explanation
Indices: 1179607--1179652 Score: 56
Period size: 6 Copynumber: 7.5 Consensus size: 6
1179597 AAACATAATG
* * *
1179607 AATAAA ATTAAA ATTAAA AATAAC AATAAA AATGAAA AATAAA AAT
1 AATAAA AATAAA AATAAA AATAAA AATAAA AAT-AAA AATAAA AAT
1179653 TTCAAAACTT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
6 29 0.83
7 6 0.17
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.22
Consensus pattern (6 bp):
AATAAA
Found at i:1181414 original size:19 final size:19
Alignment explanation
Indices: 1181390--1181432 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
1181380 CATTGACCTG
* *
1181390 TTGACTTTGATAGTTGACT
1 TTGACTTTAACAGTTGACT
1181409 TTGACTTTAACAGTTGACT
1 TTGACTTTAACAGTTGACT
1181428 TTGAC
1 TTGAC
1181433 CCTATCTTGC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.23, C:0.14, G:0.19, T:0.44
Consensus pattern (19 bp):
TTGACTTTAACAGTTGACT
Found at i:1196661 original size:15 final size:16
Alignment explanation
Indices: 1196641--1196673 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1196631 GTCCGGGCCC
*
1196641 AAACC-AAATCAAAAT
1 AAACCAAAATAAAAAT
1196656 AAACCAAAATAAAAAT
1 AAACCAAAATAAAAAT
1196672 AA
1 AA
1196674 TAAAATTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.73, C:0.15, G:0.00, T:0.12
Consensus pattern (16 bp):
AAACCAAAATAAAAAT
Found at i:1198476 original size:30 final size:30
Alignment explanation
Indices: 1198440--1198499 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
1198430 ACTATGCATA
1198440 ATATCATCATGCATAACCGATTCCCATTTT
1 ATATCATCATGCATAACCGATTCCCATTTT
1198470 ATATCATCATGCATAACCGATTCCCATTTT
1 ATATCATCATGCATAACCGATTCCCATTTT
1198500 CCTTTGATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.30, C:0.27, G:0.07, T:0.37
Consensus pattern (30 bp):
ATATCATCATGCATAACCGATTCCCATTTT
Found at i:1198714 original size:22 final size:25
Alignment explanation
Indices: 1198660--1198712 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
1198650 AAATCCAAAG
1198660 TAATAAATCGTGCCCAGTGTTATAA
1 TAATAAATCGTGCCCAGTGTTATAA
1198685 TAATAAATCGTGCCCAGTGTTATAA
1 TAATAAATCGTGCCCAGTGTTATAA
1198710 TAA
1 TAA
1198713 ATGACACCTA
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:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (25 bp):
TAATAAATCGTGCCCAGTGTTATAA
Found at i:1203542 original size:32 final size:32
Alignment explanation
Indices: 1203506--1203568 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
1203496 AGCTGAAATT
* *
1203506 AATTAGCTGATTAATGTGTTTCAGGTACATGC
1 AATTAGCTGATTAATATATTTCAGGTACATGC
1203538 AATTAGCTGATTAATATATTTCAGGTACATG
1 AATTAGCTGATTAATATATTTCAGGTACATG
1203569 TATGGATGGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.32, C:0.11, G:0.19, T:0.38
Consensus pattern (32 bp):
AATTAGCTGATTAATATATTTCAGGTACATGC
Found at i:1206828 original size:13 final size:14
Alignment explanation
Indices: 1206809--1206847 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
1206799 GCAAAGAAAG
1206809 TGAAAAGAAAGAGA
1 TGAAAAGAAAGAGA
*
1206823 -GAAAAGAAAAAGA
1 TGAAAAGAAAGAGA
*
1206836 TGAAAAGGAAGA
1 TGAAAAGAAAGA
1206848 AAAAGAGATA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
13 12 0.57
14 9 0.43
ACGTcount: A:0.67, C:0.00, G:0.28, T:0.05
Consensus pattern (14 bp):
TGAAAAGAAAGAGA
Found at i:1209915 original size:547 final size:537
Alignment explanation
Indices: 1208881--1209964 Score: 2078
Period size: 547 Copynumber: 2.0 Consensus size: 537
1208871 CAATTTATTT
1208881 TTTAGGGAAATCGTTCGATTGCATGGCATTTCGAGAACCATCGTATCTGATCGAGACACGAAATT
1 TTTAGGGAAATCGTTCGATTGCATGGCATTTCGAGAACCATCGTATCTGATCGAGACACGAAATT
1208946 TCTTAGTCATTTCTGGAGGTCGTTGTGGGGAAAGCTTGGAACGAAGCTACTGTTCTCAACAACTT
66 TCTTAGTCATTTCTGGAGGTCGTTGTGGGGAAAGCTTGGAACGAAGCTACTGTTCTCAACAACTT
1209011 GTCACCCCCAAACGGATGGCCAAATGGAGGTGGTGAATCGTGTTTTGTCAACCTTGTTGCGAGCT
131 GTCACCCCCAAACGGATGGCCAAATGGAGGTGGTGAATCGTGTTTTGTCAACCTTGTTGCGAGCT
1209076 ATCATTCAGAAAAATCTAAAGTCGTGAGAGGAGTGTTTGCCGCACATCGAGTTCGCTTACAATAG
196 ATCATTCAGAAAAATCTAAAGTCGTGAGAGGAGTGTTTGCCGCACATCGAGTTCGCTTACAATAG
1209141 ATTCATTCATTCGGCAATCAAACACTCACCTTTTAAAATTGTTTATGGTTTTAATCCCTTGACTC
261 ATTCATTCATTCGGCAATCAAACACTCACCTTTTAAAATTGTTTATGGTTTTAATCCCTTGACTC
1209206 CATTAGACTTAGTTCCTTTGCCTAATGATCAGCTTATTCATGTAAATGCTAAGCGGAAGGCTGAG
326 CATTAGACTTAGTTCCTTTGCCTAATGATCAGCTTATTCATGTAAATGCTAAGCGGAAGGCTGAG
1209271 TACGTGAAGCAGCTACATCAAAAAGTGAGAGACAATATTGAGGCTAGAACCGAAAGCTACATGCA
391 TACGTGAAGCAGCTACATCAAAAAGTGAGAGACAATATTGAGGCTAGAACCGAAAGCTACATGCA
1209336 CAAGGTAAATAAGGGACAAAAATGTGTTATGTTCGAACTCGGAGATTGGGTTTGGGTTCACATGA
456 CAAGGTAAATAAGGGACAAAAATGTGTTATGTTCGAACTCGGAGATTGGGTTTGGGTTCACATGA
1209401 GAAAGGAGCGTTTCCCA
521 GAAAGGAGCGTTTCCCA
1209418 NNNNNNNNNNTTTAGGGAAATCGTTCGATTGCATGGCATTTCGAGAACCATCGTATCTGATCGAG
1 ----------TTTAGGGAAATCGTTCGATTGCATGGCATTTCGAGAACCATCGTATCTGATCGAG
1209483 ACACGAAATTTCTTAGTCATTTCTGGAGGTCGTTGTGGGGAAAGCTTGGAACGAAGCTACTGTTC
56 ACACGAAATTTCTTAGTCATTTCTGGAGGTCGTTGTGGGGAAAGCTTGGAACGAAGCTACTGTTC
1209548 TCAACAACTTGTCACCCCCAAACGGATGGCCAAATGGAGGTGGTGAATCGTGTTTTGTCAACCTT
121 TCAACAACTTGTCACCCCCAAACGGATGGCCAAATGGAGGTGGTGAATCGTGTTTTGTCAACCTT
1209613 GTTGCGAGCTATCATTCAGAAAAATCTAAAGTCGTGAGAGGAGTGTTTGCCGCACATCGAGTTCG
186 GTTGCGAGCTATCATTCAGAAAAATCTAAAGTCGTGAGAGGAGTGTTTGCCGCACATCGAGTTCG
1209678 CTTACAATAGATTCATTCATTCGGCAATCAAACACTCACCTTTTAAAATTGTTTATGGTTTTAAT
251 CTTACAATAGATTCATTCATTCGGCAATCAAACACTCACCTTTTAAAATTGTTTATGGTTTTAAT
1209743 CCCTTGACTCCATTAGACTTAGTTCCTTTGCCTAATGATCAGCTTATTCATGTAAATGCTAAGCG
316 CCCTTGACTCCATTAGACTTAGTTCCTTTGCCTAATGATCAGCTTATTCATGTAAATGCTAAGCG
1209808 GAAGGCTGAGTACGTGAAGCAGCTACATCAAAAAGTGAGAGACAATATTGAGGCTAGAACCGAAA
381 GAAGGCTGAGTACGTGAAGCAGCTACATCAAAAAGTGAGAGACAATATTGAGGCTAGAACCGAAA
1209873 GCTACATGCACAAGGTAAATAAGGGACAAAAATGTGTTATGTTCGAACTCGGAGATTGGGTTTGG
446 GCTACATGCACAAGGTAAATAAGGGACAAAAATGTGTTATGTTCGAACTCGGAGATTGGGTTTGG
1209938 GTTCACATGAGAAAGGAGCGTTTCCCA
511 GTTCACATGAGAAAGGAGCGTTTCCCA
1209965 GCCCAACGAA
Statistics
Matches: 537, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
547 537 1.00
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.28
Consensus pattern (537 bp):
TTTAGGGAAATCGTTCGATTGCATGGCATTTCGAGAACCATCGTATCTGATCGAGACACGAAATT
TCTTAGTCATTTCTGGAGGTCGTTGTGGGGAAAGCTTGGAACGAAGCTACTGTTCTCAACAACTT
GTCACCCCCAAACGGATGGCCAAATGGAGGTGGTGAATCGTGTTTTGTCAACCTTGTTGCGAGCT
ATCATTCAGAAAAATCTAAAGTCGTGAGAGGAGTGTTTGCCGCACATCGAGTTCGCTTACAATAG
ATTCATTCATTCGGCAATCAAACACTCACCTTTTAAAATTGTTTATGGTTTTAATCCCTTGACTC
CATTAGACTTAGTTCCTTTGCCTAATGATCAGCTTATTCATGTAAATGCTAAGCGGAAGGCTGAG
TACGTGAAGCAGCTACATCAAAAAGTGAGAGACAATATTGAGGCTAGAACCGAAAGCTACATGCA
CAAGGTAAATAAGGGACAAAAATGTGTTATGTTCGAACTCGGAGATTGGGTTTGGGTTCACATGA
GAAAGGAGCGTTTCCCA
Found at i:1210681 original size:32 final size:32
Alignment explanation
Indices: 1210621--1210683 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
1210611 AGCTGAAATT
* *
1210621 AATTAGCTGATTAATGTGTTTCAGGTACATGC
1 AATTAGCTGATTAATATATTTCAGGTACATGC
1210653 AATTAGCTGATTAATATATTTCTA-GTACATG
1 AATTAGCTGATTAATATATTTC-AGGTACATG
1210684 TATGGATGGC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 27 0.96
33 1 0.04
ACGTcount: A:0.32, C:0.11, G:0.17, T:0.40
Consensus pattern (32 bp):
AATTAGCTGATTAATATATTTCAGGTACATGC
Found at i:1220834 original size:18 final size:18
Alignment explanation
Indices: 1220813--1220853 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1220803 GATTTCACCC
*
1220813 AAAAAGAAGA-AAAAGAGA
1 AAAAAG-AGACAAAAAAGA
1220831 AAAAAGAGACAAAAAAGA
1 AAAAAGAGACAAAAAAGA
1220849 AAAAA
1 AAAAA
1220854 AAAGGAGAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 3 0.14
18 18 0.86
ACGTcount: A:0.80, C:0.02, G:0.17, T:0.00
Consensus pattern (18 bp):
AAAAAGAGACAAAAAAGA
Found at i:1220855 original size:9 final size:9
Alignment explanation
Indices: 1220813--1220855 Score: 50
Period size: 9 Copynumber: 4.6 Consensus size: 9
1220803 GATTTCACCC
1220813 AAAAAGAAGA
1 AAAAAGAA-A
1220823 AAAAGAGAAA
1 AAAA-AGAAA
* *
1220833 AAAGAGACA
1 AAAAAGAAA
1220842 AAAAAGAAA
1 AAAAAGAAA
1220851 AAAAA
1 AAAAA
1220856 AGGAGAGGTC
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
9 16 0.57
10 8 0.29
11 4 0.14
ACGTcount: A:0.81, C:0.02, G:0.16, T:0.00
Consensus pattern (9 bp):
AAAAAGAAA
Found at i:1222256 original size:39 final size:39
Alignment explanation
Indices: 1222208--1222346 Score: 107
Period size: 39 Copynumber: 3.6 Consensus size: 39
1222198 TCATCATCTA
* * * **
1222208 ATCTCTTACCCCGATCGTGGGGTAGATTACAGCTACCTT
1 ATCTTTTACCCCGATCATGGGGTAGATTACAGCCACCCG
* * * *
1222247 ATCTTTTACCCCTATCATGGGGCAAATTGCAGCCACCCG
1 ATCTTTTACCCCGATCATGGGGTAGATTACAGCCACCCG
* * * ** * * *
1222286 ATCGTATACCCCGATCATGGGGTAGGTTGTATCCATCCA
1 ATCTTTTACCCCGATCATGGGGTAGATTACAGCCACCCG
* *
1222325 ATCTCTTATCCCGATCATGGGG
1 ATCTTTTACCCCGATCATGGGG
1222347 CAAATTGCAA
Statistics
Matches: 77, Mismatches: 23, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
39 77 1.00
ACGTcount: A:0.22, C:0.29, G:0.21, T:0.29
Consensus pattern (39 bp):
ATCTTTTACCCCGATCATGGGGTAGATTACAGCCACCCG
Found at i:1222723 original size:208 final size:208
Alignment explanation
Indices: 1222364--1222827 Score: 723
Period size: 208 Copynumber: 2.2 Consensus size: 208
1222354 CAATCATCCG
** * * * *
1222364 AAGCAATAAAGTGGTTATCTTCCTGATGAGATGCAGAGAAGTGAACCAAATCTGTCTTTCTGATG
1 AAGCAATAAAACGGTCATCTTCCTGATGAGATACAGAGAAGTGGACCAAATCTGTCTTCCTGATG
*
1222429 AGATACACAGAAGTGGATTAAATCAATGAGGCAGTCATCTTCTTGATGAGATACAGAGAAGTAGA
66 AGATACACAGAAGTGGATTAAATCAATGAGGCAGTCATCTTCCTGATGAGATACAGAGAAGTAGA
*
1222494 CTAAATCAATGAAGCGAAGCTCAATACGAATGAGACTTCAAACCCCATCTTCTTGATGAGATACA
131 CCAAATCAATGAAGCGAAGCTCAATACGAATGAGACTTCAAACCCCATCTTCTTGATGAGATACA
*
1222559 TAAAAGTGGGTCA
196 GAAAAGTGGGTCA
*
1222572 AAGCAATAAAACGGTCATCTTCCTGATGAAATACAGAGAAGTGGACCAAATCTGTCTTCCTGATG
1 AAGCAATAAAACGGTCATCTTCCTGATGAGATACAGAGAAGTGGACCAAATCTGTCTTCCTGATG
* * *
1222637 AGATACAGAGTAGTGGATTGAAA-CAATGAGGCAGTTATCTTCCTGATGAGATACAGAGAAGTAG
66 AGATACACAGAAGTGGATT-AAATCAATGAGGCAGTCATCTTCCTGATGAGATACAGAGAAGTAG
*
1222701 ACCAAATCAATGAAGTGAAGCTCAATACGAATGAGACTTCAAACCCCATCTTCTTGATGAGATAC
130 ACCAAATCAATGAAGCGAAGCTCAATACGAATGAGACTTCAAACCCCATCTTCTTGATGAGATAC
* *
1222766 AGAGAAGTGGGTTA
195 AGAAAAGTGGGTCA
* * ** *
1222780 AAACAATGAAACAATCATCTTCCTAATGAGATACAGAGAAGTGGACCA
1 AAGCAATAAAACGGTCATCTTCCTGATGAGATACAGAGAAGTGGACCA
1222828 GAGATGAAGC
Statistics
Matches: 233, Mismatches: 22, Indels: 2
0.91 0.09 0.01
Matches are distributed among these distances:
208 230 0.99
209 3 0.01
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.24
Consensus pattern (208 bp):
AAGCAATAAAACGGTCATCTTCCTGATGAGATACAGAGAAGTGGACCAAATCTGTCTTCCTGATG
AGATACACAGAAGTGGATTAAATCAATGAGGCAGTCATCTTCCTGATGAGATACAGAGAAGTAGA
CCAAATCAATGAAGCGAAGCTCAATACGAATGAGACTTCAAACCCCATCTTCTTGATGAGATACA
GAAAAGTGGGTCA
Found at i:1225103 original size:22 final size:22
Alignment explanation
Indices: 1225075--1225126 Score: 95
Period size: 22 Copynumber: 2.4 Consensus size: 22
1225065 ATCTATATAA
1225075 TTGTTTATTTTATGTATTACCT
1 TTGTTTATTTTATGTATTACCT
1225097 TTGTTTATTTTATGTATTACCT
1 TTGTTTATTTTATGTATTACCT
*
1225119 TTCTTTAT
1 TTGTTTAT
1225127 GTGTTTTGGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.17, C:0.10, G:0.08, T:0.65
Consensus pattern (22 bp):
TTGTTTATTTTATGTATTACCT
Found at i:1226373 original size:24 final size:26
Alignment explanation
Indices: 1226346--1226408 Score: 64
Period size: 24 Copynumber: 2.6 Consensus size: 26
1226336 GCACAAAATT
* *
1226346 TTCTTCAT-TTTCTTTTTC-CTTTTC
1 TTCTTCATCCTTCTTCTTCTCTTTTC
1226370 TTC-TCATCCTTCTTCTTCTCTTTTC
1 TTCTTCATCCTTCTTCTTCTCTTTTC
*
1226395 -TCTTCTTCC-TCTTC
1 TTCTTCATCCTTCTTC
1226409 AACACCCACT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
23 4 0.12
24 18 0.55
25 11 0.33
ACGTcount: A:0.03, C:0.33, G:0.00, T:0.63
Consensus pattern (26 bp):
TTCTTCATCCTTCTTCTTCTCTTTTC
Found at i:1232020 original size:16 final size:16
Alignment explanation
Indices: 1231989--1232021 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1231979 CGATCACAGA
1231989 ACTCGATGCAGTCCAT
1 ACTCGATGCAGTCCAT
1232005 ACTCAGATGCAG-CCAT
1 ACTC-GATGCAGTCCAT
1232021 A
1 A
1232022 AGTTCGAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.30, C:0.30, G:0.18, T:0.21
Consensus pattern (16 bp):
ACTCGATGCAGTCCAT
Found at i:1241908 original size:15 final size:15
Alignment explanation
Indices: 1241888--1241924 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
1241878 TGATTGTAAC
1241888 TCCCTTGTCGAAAGT
1 TCCCTTGTCGAAAGT
1241903 TCCCTTGTCGAAAGT
1 TCCCTTGTCGAAAGT
1241918 TCCCTTG
1 TCCCTTG
1241925 ATTTGAGGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.16, C:0.30, G:0.19, T:0.35
Consensus pattern (15 bp):
TCCCTTGTCGAAAGT
Found at i:1252252 original size:14 final size:15
Alignment explanation
Indices: 1252227--1252256 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
1252217 TTTTCTACAT
1252227 TTAACTATTCAACAC
1 TTAACTATTCAACAC
1252242 TTAAC-ATTCAACAC
1 TTAACTATTCAACAC
1252256 T
1 T
1252257 ATTTGATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.40, C:0.27, G:0.00, T:0.33
Consensus pattern (15 bp):
TTAACTATTCAACAC
Found at i:1259892 original size:9 final size:9
Alignment explanation
Indices: 1259878--1259913 Score: 56
Period size: 9 Copynumber: 4.0 Consensus size: 9
1259868 GAGAAGGAAG
1259878 AAGAAGAAA
1 AAGAAGAAA
1259887 AAGAAGAAA
1 AAGAAGAAA
1259896 AAGAA-AAA
1 AAGAAGAAA
1259904 AAGAATGAAA
1 AAGAA-GAAA
1259914 TGAAGGAACC
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
8 8 0.32
9 14 0.56
10 3 0.12
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.03
Consensus pattern (9 bp):
AAGAAGAAA
Found at i:1269334 original size:52 final size:51
Alignment explanation
Indices: 1269201--1269374 Score: 214
Period size: 52 Copynumber: 3.5 Consensus size: 51
1269191 AAAAGGTGTG
* * *
1269201 ATAACTATGTGTCATTGTGAGTATATGAATCCTTTACGGATAATGAGGTTC
1 ATAACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCC
*
1269252 --AA-TA--TGTCATCATGAGTATATGAATCCTTTACGGATTATGAGGTCC
1 ATAACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCC
* * *
1269298 AATAACTATCTGTCATCGTGAGTATATGATTCCTTTACGGATTAAGAGGTCC
1 -ATAACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCC
* *
1269350 GATGACTATGTGCCATCGTGAGTAT
1 -ATAACTATGTGTCATCGTGAGTAT
1269375 TAAATGCAAT
Statistics
Matches: 106, Mismatches: 11, Indels: 11
0.83 0.09 0.09
Matches are distributed among these distances:
46 38 0.36
48 2 0.02
49 4 0.04
50 2 0.02
52 60 0.57
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.35
Consensus pattern (51 bp):
ATAACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCC
Found at i:1276376 original size:62 final size:62
Alignment explanation
Indices: 1276277--1276403 Score: 209
Period size: 62 Copynumber: 2.0 Consensus size: 62
1276267 TCCGATGACT
* *
1276277 ATGTGTCATTGTGAGTATATGAATCCTTTACGAATTATGAGGTCCGACGACTATGTGTCATC
1 ATGTGTCATCGTGAGTATATGAATCCTTTACGAATTATGAGGTCCAACGACTATGTGTCATC
* * *
1276339 ATGTGTCATCGTGAGTATATGAATCTTTTACGGATTATGAGGTCCAATGACTATGTGTCATC
1 ATGTGTCATCGTGAGTATATGAATCCTTTACGAATTATGAGGTCCAACGACTATGTGTCATC
1276401 ATG
1 ATG
1276404 AGTGTAACAT
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
62 60 1.00
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.36
Consensus pattern (62 bp):
ATGTGTCATCGTGAGTATATGAATCCTTTACGAATTATGAGGTCCAACGACTATGTGTCATC
Found at i:1280365 original size:22 final size:21
Alignment explanation
Indices: 1280335--1280376 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
1280325 CAGTACTTCT
*
1280335 CCAAAGGTACTTATACATCTC
1 CCAAAGGTACCTATACATCTC
*
1280356 CCAAGAGGTACCTGTACATCT
1 CCAA-AGGTACCTATACATCT
1280377 TTAGAGGTAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (21 bp):
CCAAAGGTACCTATACATCTC
Found at i:1280541 original size:22 final size:22
Alignment explanation
Indices: 1280516--1280564 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
1280506 GCCTCAAAAT
*
1280516 TTTTCTAAACTTGATTTT-ATGA
1 TTTTCTAAA-TTGATTTTCAAGA
* *
1280538 TTTTATAAATTTATTTTCAAGA
1 TTTTCTAAATTGATTTTCAAGA
1280560 TTTTC
1 TTTTC
1280565 GTTTCGTTTG
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 7 0.32
22 15 0.68
ACGTcount: A:0.29, C:0.08, G:0.06, T:0.57
Consensus pattern (22 bp):
TTTTCTAAATTGATTTTCAAGA
Found at i:1280844 original size:91 final size:91
Alignment explanation
Indices: 1280725--1280906 Score: 355
Period size: 91 Copynumber: 2.0 Consensus size: 91
1280715 TACATAGTTT
*
1280725 TACTCTTTTTTTTAAACACATATAAGAATATTACGTGGAAATTAATTTCCCCAAAAATTTAAAAC
1 TACTCTTTTTTTAAAACACATATAAGAATATTACGTGGAAATTAATTTCCCCAAAAATTTAAAAC
1280790 AAATGTGTTAGCTTGATGGATTAAAC
66 AAATGTGTTAGCTTGATGGATTAAAC
1280816 TACTCTTTTTTTAAAACACATATAAGAATATTACGTGGAAATTAATTTCCCCAAAAATTTAAAAC
1 TACTCTTTTTTTAAAACACATATAAGAATATTACGTGGAAATTAATTTCCCCAAAAATTTAAAAC
1280881 AAATGTGTTAGCTTGATGGATTAAAC
66 AAATGTGTTAGCTTGATGGATTAAAC
1280907 CAAAATTGCC
Statistics
Matches: 90, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
91 90 1.00
ACGTcount: A:0.40, C:0.13, G:0.11, T:0.36
Consensus pattern (91 bp):
TACTCTTTTTTTAAAACACATATAAGAATATTACGTGGAAATTAATTTCCCCAAAAATTTAAAAC
AAATGTGTTAGCTTGATGGATTAAAC
Found at i:1281876 original size:19 final size:19
Alignment explanation
Indices: 1281844--1281902 Score: 64
Period size: 19 Copynumber: 3.0 Consensus size: 19
1281834 ATTTTGGAGT
*
1281844 GTTAAAATGATTTTGACTTG
1 GTTAAAAT-CTTTTGACTTG
*
1281864 GTTGAAATCTTTTGACTTG
1 GTTAAAATCTTTTGACTTG
* *
1281883 TTTAAAATCATTTGAACTTG
1 GTTAAAATCTTTTG-ACTTG
1281903 ATTTTAAATT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
19 21 0.64
20 12 0.36
ACGTcount: A:0.29, C:0.08, G:0.17, T:0.46
Consensus pattern (19 bp):
GTTAAAATCTTTTGACTTG
Found at i:1281916 original size:21 final size:19
Alignment explanation
Indices: 1281845--1281916 Score: 63
Period size: 19 Copynumber: 3.6 Consensus size: 19
1281835 TTTTGGAGTG
* *
1281845 TTAAAATGATTTTGACTTGG
1 TTAAAATCA-TTTGACTTGT
* *
1281865 TTGAAATCTTTTGACTTGT
1 TTAAAATCATTTGACTTGT
1281884 TTAAAATCATTTGAACTTGAT
1 TTAAAATCATTTG-ACTTG-T
* *
1281905 TTTAAATTATTT
1 TTAAAATCATTT
1281917 CAAAATTTTC
Statistics
Matches: 42, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
19 20 0.48
20 11 0.26
21 11 0.26
ACGTcount: A:0.31, C:0.07, G:0.12, T:0.50
Consensus pattern (19 bp):
TTAAAATCATTTGACTTGT
Found at i:1290433 original size:28 final size:28
Alignment explanation
Indices: 1290401--1290456 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
1290391 CTCGTTACCT
*
1290401 TAGCATTTTCTCGGTTAGTCTCACTATC
1 TAGCATTTTCTCGATTAGTCTCACTATC
1290429 TAGCATTTTCTCGATTAGTCTCACTATC
1 TAGCATTTTCTCGATTAGTCTCACTATC
1290457 GAGCCATCCC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.20, C:0.25, G:0.12, T:0.43
Consensus pattern (28 bp):
TAGCATTTTCTCGATTAGTCTCACTATC
Found at i:1292286 original size:120 final size:117
Alignment explanation
Indices: 1292065--1292278 Score: 286
Period size: 120 Copynumber: 1.8 Consensus size: 117
1292055 CTTGTCCCCA
* * * * * * * *
1292065 CAAACTCTTTTGGTTTTGTGACATCCTTTAATGTTGCACTTGACACTCCATTCCCTATGACTGCT
1 CAAACTCTTTCGGCTTTGGGACATCCATTAATGCTGCACTTAACACTCCATTCCCCACGACTGCT
* * *
1292130 CGACACAAGGCAAGCTCTCCCTCGAGCTCCCCCAATCCAGACCTTATCCTCG
66 CAACACAAGGCAAACTCTCCCTCGAGCACCCCCAATCCAGACCTTATCCTCG
1292182 CAAACTCTTTCGGCTTTGGGACAT-CATTAAGTGCTGCACTTAACACTCCTTCATTCCCCACGAC
1 CAAACTCTTTCGGCTTTGGGACATCCATTAA-TGCTGCACTTAACACT-C--CATTCCCCACGAC
1292246 TGCTCAACACAAGGCAAACTCTCCCTCGAGCAC
62 TGCTCAACACAAGGCAAACTCTCCCTCGAGCAC
1292279 TTTCAATCTT
Statistics
Matches: 82, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
116 5 0.06
117 35 0.43
118 1 0.01
120 41 0.50
ACGTcount: A:0.23, C:0.35, G:0.14, T:0.28
Consensus pattern (117 bp):
CAAACTCTTTCGGCTTTGGGACATCCATTAATGCTGCACTTAACACTCCATTCCCCACGACTGCT
CAACACAAGGCAAACTCTCCCTCGAGCACCCCCAATCCAGACCTTATCCTCG
Found at i:1298328 original size:18 final size:19
Alignment explanation
Indices: 1298289--1298328 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
1298279 ATTGCTTCTC
*
1298289 AAAATCACTTTTGAGACAA
1 AAAAGCACTTTTGAGACAA
*
1298308 AAAAGCACTTTTGAGATAA
1 AAAAGCACTTTTGAGACAA
1298327 AA
1 AA
1298329 GCATTACTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.50, C:0.12, G:0.12, T:0.25
Consensus pattern (19 bp):
AAAAGCACTTTTGAGACAA
Found at i:1306128 original size:22 final size:20
Alignment explanation
Indices: 1306090--1306161 Score: 56
Period size: 22 Copynumber: 3.4 Consensus size: 20
1306080 TATATAAGTA
1306090 TATT-TTTAATATTTATTGT
1 TATTATTTAATATTTATTGT
*
1306109 TATTATTTGAATATTGTATTAT
1 TATTATTT-AATATT-TATTGT
* * *
1306131 TTTTATTTTATTATTAATTTTGT
1 TATTA-TTTAATATT--TATTGT
1306154 TATTATTT
1 TATTATTT
1306162 TAAAGATGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
19 4 0.10
20 3 0.07
21 6 0.15
22 17 0.41
23 11 0.27
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (20 bp):
TATTATTTAATATTTATTGT
Found at i:1306164 original size:17 final size:17
Alignment explanation
Indices: 1306103--1306164 Score: 64
Period size: 14 Copynumber: 4.0 Consensus size: 17
1306093 TTTTAATATT
*
1306103 TATTGTTATTATTTGAA
1 TATTGTTATTATTTTAA
1306120 TATTG-TATTATTTT--
1 TATTGTTATTATTTTAA
1306134 TATT-TTATTA--TTAA
1 TATTGTTATTATTTTAA
*
1306148 TTTTGTTATTATTTTAA
1 TATTGTTATTATTTTAA
1306165 AGATGTTTGC
Statistics
Matches: 37, Mismatches: 2, Indels: 12
0.73 0.04 0.24
Matches are distributed among these distances:
12 2 0.05
14 12 0.32
15 6 0.16
16 8 0.22
17 9 0.24
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.66
Consensus pattern (17 bp):
TATTGTTATTATTTTAA
Found at i:1306507 original size:3 final size:3
Alignment explanation
Indices: 1306499--1306525 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1306489 TGAATTTTAT
1306499 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1306526 CAAGAAGCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1313018 original size:36 final size:36
Alignment explanation
Indices: 1312978--1313087 Score: 155
Period size: 36 Copynumber: 3.3 Consensus size: 36
1312968 TTAGGTCACC
1312978 AGGGAGTAAAATGAGCATCATGACCTTTGGGTCAAT
1 AGGGAGTAAAATGAGCATCATGACCTTTGGGTCAAT
*
1313014 AGGGAGTAAAATGAGCATCATTACCTTTGGGTCAAT
1 AGGGAGTAAAATGAGCATCATGACCTTTGGGTCAAT
1313050 AGGGAGT---A--AG---CATGACCTTTGGGTCAAT
1 AGGGAGTAAAATGAGCATCATGACCTTTGGGTCAAT
1313078 AGGGAGTAAA
1 AGGGAGTAAA
1313088 TCGGATATTG
Statistics
Matches: 69, Mismatches: 2, Indels: 11
0.84 0.02 0.13
Matches are distributed among these distances:
28 24 0.35
31 2 0.03
33 1 0.01
36 42 0.61
ACGTcount: A:0.34, C:0.13, G:0.29, T:0.25
Consensus pattern (36 bp):
AGGGAGTAAAATGAGCATCATGACCTTTGGGTCAAT
Found at i:1315067 original size:2 final size:2
Alignment explanation
Indices: 1315060--1315085 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1315050 GTGATTGAAC
1315060 CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA
1315086 TATATAATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Done.